AutoCloner

Multiple sequence alignment - TraesCS1D01G261900

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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	TraesCS1D01G261900	chr1D	100.000	2649	0	0	1	2649	355824235	355826883	0.000000e+00	4892.0
1	TraesCS1D01G261900	chr1D	83.104	1965	147	97	779	2649	446436834	446438707	0.000000e+00	1618.0
2	TraesCS1D01G261900	chr1D	82.612	1225	97	58	1484	2645	445385242	445384071	0.000000e+00	976.0
3	TraesCS1D01G261900	chr1D	85.661	809	67	36	752	1546	445387273	445386500	0.000000e+00	806.0
4	TraesCS1D01G261900	chr1D	87.057	734	66	15	751	1479	446558190	446558899	0.000000e+00	802.0
5	TraesCS1D01G261900	chr1D	87.425	167	16	4	744	906	445317306	445317471	1.250000e-43	187.0
6	TraesCS1D01G261900	chr1A	88.389	1645	83	45	260	1862	456650214	456651792	0.000000e+00	1881.0
7	TraesCS1D01G261900	chr1A	84.627	1340	115	43	1033	2326	541319304	541320598	0.000000e+00	1249.0
8	TraesCS1D01G261900	chr1A	85.440	989	85	34	752	1721	541463642	541462694	0.000000e+00	974.0
9	TraesCS1D01G261900	chr1A	85.948	733	65	26	752	1477	542358199	542358900	0.000000e+00	749.0
10	TraesCS1D01G261900	chr1A	96.094	256	5	2	2399	2649	456652235	456652490	1.900000e-111	412.0
11	TraesCS1D01G261900	chr1A	92.391	276	9	6	2140	2403	456651932	456652207	1.490000e-102	383.0
12	TraesCS1D01G261900	chr1A	92.941	255	18	0	1	255	456650005	456650259	3.220000e-99	372.0
13	TraesCS1D01G261900	chr1A	84.078	358	26	14	2260	2591	541462285	541461933	1.530000e-82	316.0
14	TraesCS1D01G261900	chr1A	86.607	112	4	3	1861	1961	456651819	456651930	2.160000e-21	113.0
15	TraesCS1D01G261900	chr1B	85.705	1623	128	48	757	2331	608054128	608052562	0.000000e+00	1616.0
16	TraesCS1D01G261900	chr1B	84.775	1353	100	42	1060	2343	610560760	610562075	0.000000e+00	1260.0
17	TraesCS1D01G261900	chr1B	83.797	1185	86	52	1038	2146	607429557	607428403	0.000000e+00	1027.0
18	TraesCS1D01G261900	chr1B	88.976	635	53	8	1129	1753	608355308	608354681	0.000000e+00	769.0
19	TraesCS1D01G261900	chr1B	82.963	540	42	24	2117	2610	608354449	608353914	2.420000e-120	442.0
20	TraesCS1D01G261900	chr1B	89.347	291	18	4	2371	2649	610562077	610562366	1.170000e-93	353.0
21	TraesCS1D01G261900	chr1B	81.905	315	24	11	2359	2643	607428251	607427940	4.410000e-58	235.0
22	TraesCS1D01G261900	chr1B	90.850	153	13	1	751	902	606839638	606839790	1.240000e-48	204.0
23	TraesCS1D01G261900	chr1B	89.024	164	16	2	744	905	607429802	607429639	4.470000e-48	202.0
24	TraesCS1D01G261900	chr1B	82.500	160	25	3	779	936	611131219	611131377	1.280000e-28	137.0
25	TraesCS1D01G261900	chr1B	77.778	207	14	11	2434	2610	608051897	608051693	6.030000e-17	99.0
26	TraesCS1D01G261900	chr1B	94.118	51	3	0	675	725	608054179	608054129	7.860000e-11	78.7
27	TraesCS1D01G261900	chr1B	96.875	32	1	0	1806	1837	608354651	608354620	1.000000e-03	54.7
28	TraesCS1D01G261900	chr2B	91.499	647	33	17	1035	1681	161026441	161027065	0.000000e+00	870.0
29	TraesCS1D01G261900	chr2B	77.764	796	54	51	1774	2515	161027157	161027883	2.490000e-100	375.0
30	TraesCS1D01G261900	chr3D	89.458	664	39	18	1038	1689	114883129	114882485	0.000000e+00	809.0
31	TraesCS1D01G261900	chr3D	92.913	127	9	0	2	128	49010116	49009990	4.500000e-43	185.0
32	TraesCS1D01G261900	chr3B	88.393	672	41	21	1038	1689	168140448	168139794	0.000000e+00	774.0
33	TraesCS1D01G261900	chr3B	92.969	128	9	0	1	128	78607077	78606950	1.250000e-43	187.0
34	TraesCS1D01G261900	chr2A	88.532	218	24	1	8	225	773404412	773404628	2.020000e-66	263.0
35	TraesCS1D01G261900	chr3A	93.701	127	8	0	2	128	61483279	61483153	9.680000e-45	191.0
36	TraesCS1D01G261900	chr6D	78.571	154	29	4	753	904	47812113	47812264	6.030000e-17	99.0
37	TraesCS1D01G261900	chr6D	81.967	122	11	2	122	243	277850333	277850223	2.810000e-15	93.5
38	TraesCS1D01G261900	chr2D	85.294	102	5	1	134	235	637509643	637509734	2.170000e-16	97.1
39	TraesCS1D01G261900	chr4D	92.453	53	1	3	117	169	318925691	318925642	3.660000e-09	73.1
40	TraesCS1D01G261900	chr4B	92.453	53	1	3	117	169	396449429	396449380	3.660000e-09	73.1

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	TraesCS1D01G261900	chr1D	355824235	355826883	2648	False	4892.0	4892	100.000000	1	2649	1	chr1D.!!$F1	2648
1	TraesCS1D01G261900	chr1D	446436834	446438707	1873	False	1618.0	1618	83.104000	779	2649	1	chr1D.!!$F3	1870
2	TraesCS1D01G261900	chr1D	445384071	445387273	3202	True	891.0	976	84.136500	752	2645	2	chr1D.!!$R1	1893
3	TraesCS1D01G261900	chr1D	446558190	446558899	709	False	802.0	802	87.057000	751	1479	1	chr1D.!!$F4	728
4	TraesCS1D01G261900	chr1A	541319304	541320598	1294	False	1249.0	1249	84.627000	1033	2326	1	chr1A.!!$F1	1293
5	TraesCS1D01G261900	chr1A	542358199	542358900	701	False	749.0	749	85.948000	752	1477	1	chr1A.!!$F2	725
6	TraesCS1D01G261900	chr1A	541461933	541463642	1709	True	645.0	974	84.759000	752	2591	2	chr1A.!!$R1	1839
7	TraesCS1D01G261900	chr1A	456650005	456652490	2485	False	632.2	1881	91.284400	1	2649	5	chr1A.!!$F3	2648
8	TraesCS1D01G261900	chr1B	610560760	610562366	1606	False	806.5	1260	87.061000	1060	2649	2	chr1B.!!$F3	1589
9	TraesCS1D01G261900	chr1B	608051693	608054179	2486	True	597.9	1616	85.867000	675	2610	3	chr1B.!!$R2	1935
10	TraesCS1D01G261900	chr1B	607427940	607429802	1862	True	488.0	1027	84.908667	744	2643	3	chr1B.!!$R1	1899
11	TraesCS1D01G261900	chr1B	608353914	608355308	1394	True	421.9	769	89.604667	1129	2610	3	chr1B.!!$R3	1481
12	TraesCS1D01G261900	chr2B	161026441	161027883	1442	False	622.5	870	84.631500	1035	2515	2	chr2B.!!$F1	1480
13	TraesCS1D01G261900	chr3D	114882485	114883129	644	True	809.0	809	89.458000	1038	1689	1	chr3D.!!$R2	651
14	TraesCS1D01G261900	chr3B	168139794	168140448	654	True	774.0	774	88.393000	1038	1689	1	chr3B.!!$R2	651

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
471	474	0.033208	AGAGGAGAGAGGCTGACTGG	60.033	60.0	0.0	0.0	0.0	4.00	F
1000	1043	0.036306	TTTCTTCCTCTTCACCCCGC	59.964	55.0	0.0	0.0	0.0	6.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1584	3046	2.035469	ATGGGGCACAACGCATCA	59.965	55.556	0.0	0.0	45.17	3.07	R
2121	3738	2.242965	ACCAGGAATGGCATGAGATTCA	59.757	45.455	0.0	0.0	31.29	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
26	27	4.889112	CTGCGGCCTGGGCATGAT	62.889	66.667	21.03	0.00	44.11	2.45
33	34	1.884464	CCTGGGCATGATGTCGTCG	60.884	63.158	0.00	0.00	0.00	5.12
37	38	2.230940	GGCATGATGTCGTCGACGG	61.231	63.158	35.05	19.32	40.29	4.79
39	40	2.104331	ATGATGTCGTCGACGGCC	59.896	61.111	36.46	26.30	44.42	6.13
120	121	1.372499	GAGCACGTTGTACTGCCGA	60.372	57.895	1.50	0.00	33.57	5.54
124	125	0.318360	CACGTTGTACTGCCGAGTGA	60.318	55.000	6.44	0.00	33.21	3.41
132	133	3.362399	CTGCCGAGTGATCCTGCGT	62.362	63.158	0.00	0.00	0.00	5.24
282	283	3.267860	GCGAGGAGGCATTGCGAG	61.268	66.667	1.91	0.00	0.00	5.03
283	284	2.587194	CGAGGAGGCATTGCGAGG	60.587	66.667	1.91	0.00	0.00	4.63
284	285	2.203126	GAGGAGGCATTGCGAGGG	60.203	66.667	1.91	0.00	0.00	4.30
285	286	4.496336	AGGAGGCATTGCGAGGGC	62.496	66.667	3.56	3.56	40.52	5.19
328	329	3.240134	GACGGGCAGCAAGGAGACA	62.240	63.158	0.00	0.00	0.00	3.41
329	330	2.032528	CGGGCAGCAAGGAGACAA	59.967	61.111	0.00	0.00	0.00	3.18
333	334	2.970974	GCAGCAAGGAGACAACGGC	61.971	63.158	0.00	0.00	0.00	5.68
334	335	2.357517	AGCAAGGAGACAACGGCG	60.358	61.111	4.80	4.80	0.00	6.46
335	336	2.357034	GCAAGGAGACAACGGCGA	60.357	61.111	16.62	0.00	0.00	5.54
336	337	2.383527	GCAAGGAGACAACGGCGAG	61.384	63.158	16.62	8.41	0.00	5.03
337	338	1.738099	CAAGGAGACAACGGCGAGG	60.738	63.158	16.62	7.55	0.00	4.63
338	339	1.906824	AAGGAGACAACGGCGAGGA	60.907	57.895	16.62	0.00	0.00	3.71
339	340	1.878656	AAGGAGACAACGGCGAGGAG	61.879	60.000	16.62	2.16	0.00	3.69
340	341	2.182030	GAGACAACGGCGAGGAGG	59.818	66.667	16.62	0.00	0.00	4.30
341	342	3.991536	GAGACAACGGCGAGGAGGC	62.992	68.421	16.62	1.57	42.76	4.70
388	389	2.099431	GCTGTGCTTGCGGAGAGAG	61.099	63.158	0.00	0.00	0.00	3.20
391	392	1.153667	GTGCTTGCGGAGAGAGAGG	60.154	63.158	0.00	0.00	0.00	3.69
392	393	1.304464	TGCTTGCGGAGAGAGAGGA	60.304	57.895	0.00	0.00	0.00	3.71
393	394	1.318886	TGCTTGCGGAGAGAGAGGAG	61.319	60.000	0.00	0.00	0.00	3.69
394	395	1.034838	GCTTGCGGAGAGAGAGGAGA	61.035	60.000	0.00	0.00	0.00	3.71
398	399	1.214175	TGCGGAGAGAGAGGAGAGATT	59.786	52.381	0.00	0.00	0.00	2.40
431	434	3.517038	AAGTGGGTAGGGTGGGCCT	62.517	63.158	4.53	0.00	34.45	5.19
439	442	0.252974	TAGGGTGGGCCTAGCAGAAA	60.253	55.000	20.67	0.00	34.45	2.52
440	443	1.140134	AGGGTGGGCCTAGCAGAAAA	61.140	55.000	20.67	0.00	34.45	2.29
441	444	0.251608	GGGTGGGCCTAGCAGAAAAA	60.252	55.000	20.67	0.00	34.45	1.94
442	445	1.177401	GGTGGGCCTAGCAGAAAAAG	58.823	55.000	14.14	0.00	0.00	2.27
443	446	1.177401	GTGGGCCTAGCAGAAAAAGG	58.823	55.000	4.53	0.00	0.00	3.11
444	447	1.072266	TGGGCCTAGCAGAAAAAGGA	58.928	50.000	4.53	0.00	31.64	3.36
445	448	1.427368	TGGGCCTAGCAGAAAAAGGAA	59.573	47.619	4.53	0.00	31.64	3.36
446	449	2.095461	GGGCCTAGCAGAAAAAGGAAG	58.905	52.381	0.84	0.00	31.64	3.46
447	450	2.095461	GGCCTAGCAGAAAAAGGAAGG	58.905	52.381	0.00	0.00	31.64	3.46
452	455	4.223923	CCTAGCAGAAAAAGGAAGGAGAGA	59.776	45.833	0.00	0.00	31.64	3.10
471	474	0.033208	AGAGGAGAGAGGCTGACTGG	60.033	60.000	0.00	0.00	0.00	4.00
474	477	0.613292	GGAGAGAGGCTGACTGGTGA	60.613	60.000	0.00	0.00	0.00	4.02
499	502	1.135431	TGACCATGCACAAAATAGCGC	60.135	47.619	0.00	0.00	0.00	5.92
519	522	4.484872	GACGCCCTAAGTGCCCCC	62.485	72.222	0.00	0.00	0.00	5.40
522	525	3.015145	GCCCTAAGTGCCCCCTGA	61.015	66.667	0.00	0.00	0.00	3.86
546	549	3.443479	TGGGTTTGGCCTGGGGTT	61.443	61.111	3.32	0.00	37.43	4.11
559	562	2.043349	GGGTTGCCGGGGCTATTT	60.043	61.111	11.55	0.00	42.51	1.40
581	584	0.239879	TCTTGAATCCGGCGCAAAAC	59.760	50.000	10.83	0.00	0.00	2.43
595	598	2.427506	GCAAAACGATCTCTTGAGGGT	58.572	47.619	0.00	0.00	0.00	4.34
596	599	2.160417	GCAAAACGATCTCTTGAGGGTG	59.840	50.000	0.00	0.00	0.00	4.61
600	603	1.546476	ACGATCTCTTGAGGGTGTGAC	59.454	52.381	0.00	0.00	0.00	3.67
602	605	2.416566	CGATCTCTTGAGGGTGTGACTG	60.417	54.545	0.00	0.00	0.00	3.51
606	609	1.964223	TCTTGAGGGTGTGACTGAGAC	59.036	52.381	0.00	0.00	0.00	3.36
607	610	1.001406	CTTGAGGGTGTGACTGAGACC	59.999	57.143	0.00	0.00	37.27	3.85
609	612	0.605589	GAGGGTGTGACTGAGACCAG	59.394	60.000	0.00	0.00	39.96	4.00
649	653	2.340210	AAAAATGTGTTTGGTGGGGC	57.660	45.000	0.00	0.00	0.00	5.80
650	654	1.506025	AAAATGTGTTTGGTGGGGCT	58.494	45.000	0.00	0.00	0.00	5.19
661	669	2.060980	GTGGGGCTCGAGTGGAGAT	61.061	63.158	15.13	0.00	46.23	2.75
663	671	2.107953	GGGCTCGAGTGGAGATGC	59.892	66.667	15.13	0.00	46.23	3.91
665	673	1.067250	GGCTCGAGTGGAGATGCTC	59.933	63.158	15.13	0.00	46.23	4.26
671	679	0.526524	GAGTGGAGATGCTCGAACGG	60.527	60.000	0.00	0.00	0.00	4.44
673	681	0.108804	GTGGAGATGCTCGAACGGAA	60.109	55.000	0.00	0.00	0.00	4.30
800	831	1.568612	AATCACAGCACGCGAACCAG	61.569	55.000	15.93	0.29	0.00	4.00
926	969	2.683475	CCTCCAAAATCCCCCGCT	59.317	61.111	0.00	0.00	0.00	5.52
999	1042	1.339151	CCTTTCTTCCTCTTCACCCCG	60.339	57.143	0.00	0.00	0.00	5.73
1000	1043	0.036306	TTTCTTCCTCTTCACCCCGC	59.964	55.000	0.00	0.00	0.00	6.13
1544	2979	1.135972	GCGGAAATGTGTGTGCTACTG	60.136	52.381	0.00	0.00	0.00	2.74
1564	2999	8.277490	CTACTGTAGTAGTGTTCCAGAATGTA	57.723	38.462	10.25	0.00	42.22	2.29
1584	3046	3.297134	ACCTGTGTTCTTGTCATGGTT	57.703	42.857	0.00	0.00	0.00	3.67
1598	3060	1.876497	ATGGTTGATGCGTTGTGCCC	61.876	55.000	0.00	0.00	45.60	5.36
1599	3061	2.258286	GTTGATGCGTTGTGCCCC	59.742	61.111	0.00	0.00	45.60	5.80
1657	3129	5.409520	GGAAATGAAAAATGTTGGCTTCCTC	59.590	40.000	0.00	0.00	0.00	3.71
1756	3239	7.698836	TTTTGCTCTGAATTTCAGCTTTTAC	57.301	32.000	19.53	7.18	43.95	2.01
1771	3272	5.125097	CAGCTTTTACCATTCAGAGCTTGAT	59.875	40.000	0.00	0.00	38.32	2.57
1890	3443	5.706833	TGTCTGATGTTCAGTGCACATAAAT	59.293	36.000	21.04	5.69	44.58	1.40
1957	3557	7.241042	TGAACCATGCTCTAAACTAAGTACT	57.759	36.000	0.00	0.00	0.00	2.73
1958	3558	7.321153	TGAACCATGCTCTAAACTAAGTACTC	58.679	38.462	0.00	0.00	0.00	2.59
1959	3559	6.223351	ACCATGCTCTAAACTAAGTACTCC	57.777	41.667	0.00	0.00	0.00	3.85
2050	3662	2.421775	CACACCGTGCCTGCAATATTAA	59.578	45.455	0.00	0.00	0.00	1.40
2073	3690	1.066929	GTTGCATCACCCACAATTCCC	60.067	52.381	0.00	0.00	0.00	3.97
2074	3691	0.614415	TGCATCACCCACAATTCCCC	60.614	55.000	0.00	0.00	0.00	4.81
2075	3692	0.324645	GCATCACCCACAATTCCCCT	60.325	55.000	0.00	0.00	0.00	4.79
2077	3694	2.654863	CATCACCCACAATTCCCCTAC	58.345	52.381	0.00	0.00	0.00	3.18
2078	3695	0.616371	TCACCCACAATTCCCCTACG	59.384	55.000	0.00	0.00	0.00	3.51
2108	3725	2.029904	GAACATCGAGGAAGCGCTGC	62.030	60.000	12.58	9.65	31.19	5.25
2121	3738	2.045926	GCTGCCCACGATTGGTCT	60.046	61.111	0.00	0.00	42.10	3.85
2244	3894	6.317789	ACATTTGTTACATTCAGGAGTGTG	57.682	37.500	7.59	0.00	33.24	3.82
2245	3895	5.827797	ACATTTGTTACATTCAGGAGTGTGT	59.172	36.000	7.59	0.00	33.24	3.72
2246	3896	6.017109	ACATTTGTTACATTCAGGAGTGTGTC	60.017	38.462	7.59	2.20	33.24	3.67
2247	3897	4.681074	TGTTACATTCAGGAGTGTGTCA	57.319	40.909	7.59	4.39	33.24	3.58
2249	3899	5.432645	TGTTACATTCAGGAGTGTGTCAAA	58.567	37.500	7.59	0.00	33.24	2.69
2251	3901	6.545666	TGTTACATTCAGGAGTGTGTCAAAAT	59.454	34.615	7.59	0.00	33.24	1.82
2253	3903	6.469782	ACATTCAGGAGTGTGTCAAAATTT	57.530	33.333	0.00	0.00	29.74	1.82
2526	4823	3.003275	ACAAACACAGTTACAAGGATGCG	59.997	43.478	0.00	0.00	0.00	4.73

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	1.153647	GTCGACGACATCATGCCCA	60.154	57.895	22.66	0.00	32.09	5.36
99	100	2.022129	GCAGTACAACGTGCTCGCT	61.022	57.895	8.29	0.00	41.18	4.93
120	121	2.182791	CGCTCACGCAGGATCACT	59.817	61.111	0.00	0.00	35.30	3.41
124	125	2.492090	GAGACGCTCACGCAGGAT	59.508	61.111	2.53	0.00	45.53	3.24
132	133	2.358369	ACGACGAGGAGACGCTCA	60.358	61.111	0.00	0.00	41.46	4.26
184	185	2.433664	GACGAACGGGCCGTGAAT	60.434	61.111	34.87	20.68	39.99	2.57
265	266	3.267860	CTCGCAATGCCTCCTCGC	61.268	66.667	0.00	0.00	0.00	5.03
266	267	2.587194	CCTCGCAATGCCTCCTCG	60.587	66.667	0.00	0.00	0.00	4.63
267	268	2.203126	CCCTCGCAATGCCTCCTC	60.203	66.667	0.00	0.00	0.00	3.71
268	269	4.496336	GCCCTCGCAATGCCTCCT	62.496	66.667	0.00	0.00	34.03	3.69
311	312	2.818169	TTGTCTCCTTGCTGCCCGT	61.818	57.895	0.00	0.00	0.00	5.28
328	329	4.473520	CCATGCCTCCTCGCCGTT	62.474	66.667	0.00	0.00	0.00	4.44
413	416	2.127685	TAGGCCCACCCTACCCACTT	62.128	60.000	0.00	0.00	44.08	3.16
431	434	5.087323	TCTCTCTCCTTCCTTTTTCTGCTA	58.913	41.667	0.00	0.00	0.00	3.49
439	442	3.596046	TCTCTCCTCTCTCTCCTTCCTTT	59.404	47.826	0.00	0.00	0.00	3.11
440	443	3.197983	TCTCTCCTCTCTCTCCTTCCTT	58.802	50.000	0.00	0.00	0.00	3.36
441	444	2.780010	CTCTCTCCTCTCTCTCCTTCCT	59.220	54.545	0.00	0.00	0.00	3.36
442	445	2.158608	CCTCTCTCCTCTCTCTCCTTCC	60.159	59.091	0.00	0.00	0.00	3.46
443	446	2.749800	GCCTCTCTCCTCTCTCTCCTTC	60.750	59.091	0.00	0.00	0.00	3.46
444	447	1.215423	GCCTCTCTCCTCTCTCTCCTT	59.785	57.143	0.00	0.00	0.00	3.36
445	448	0.846693	GCCTCTCTCCTCTCTCTCCT	59.153	60.000	0.00	0.00	0.00	3.69
446	449	0.846693	AGCCTCTCTCCTCTCTCTCC	59.153	60.000	0.00	0.00	0.00	3.71
447	450	1.490490	TCAGCCTCTCTCCTCTCTCTC	59.510	57.143	0.00	0.00	0.00	3.20
452	455	0.033208	CCAGTCAGCCTCTCTCCTCT	60.033	60.000	0.00	0.00	0.00	3.69
471	474	1.317613	TGTGCATGGTCAAACCTCAC	58.682	50.000	0.00	4.28	39.58	3.51
474	477	4.561326	GCTATTTTGTGCATGGTCAAACCT	60.561	41.667	0.08	0.00	39.58	3.50
499	502	4.832608	GGCACTTAGGGCGTCCGG	62.833	72.222	0.00	0.00	38.33	5.14
519	522	2.036256	CAAACCCAGCCCCCTCAG	59.964	66.667	0.00	0.00	0.00	3.35
520	523	3.589542	CCAAACCCAGCCCCCTCA	61.590	66.667	0.00	0.00	0.00	3.86
528	531	3.466803	AACCCCAGGCCAAACCCAG	62.467	63.158	5.01	0.00	40.58	4.45
559	562	0.955178	TTGCGCCGGATTCAAGAAAA	59.045	45.000	5.05	0.00	0.00	2.29
562	565	0.239879	GTTTTGCGCCGGATTCAAGA	59.760	50.000	5.05	0.00	0.00	3.02
563	566	1.065031	CGTTTTGCGCCGGATTCAAG	61.065	55.000	5.05	0.00	0.00	3.02
566	569	0.588980	GATCGTTTTGCGCCGGATTC	60.589	55.000	5.05	0.00	41.07	2.52
570	573	1.635663	AAGAGATCGTTTTGCGCCGG	61.636	55.000	4.18	0.00	41.07	6.13
571	574	0.519175	CAAGAGATCGTTTTGCGCCG	60.519	55.000	4.18	0.00	41.07	6.46
573	576	1.201965	CCTCAAGAGATCGTTTTGCGC	60.202	52.381	0.00	0.00	41.07	6.09
581	584	1.821753	AGTCACACCCTCAAGAGATCG	59.178	52.381	0.00	0.00	0.00	3.69
585	588	2.029470	GTCTCAGTCACACCCTCAAGAG	60.029	54.545	0.00	0.00	0.00	2.85
590	593	0.605589	CTGGTCTCAGTCACACCCTC	59.394	60.000	0.00	0.00	36.30	4.30
600	603	2.729882	CGACGGTAAAAACTGGTCTCAG	59.270	50.000	0.00	0.00	46.10	3.35
602	605	2.064014	CCGACGGTAAAAACTGGTCTC	58.936	52.381	5.48	0.00	0.00	3.36
606	609	0.236449	GCACCGACGGTAAAAACTGG	59.764	55.000	21.25	5.74	32.11	4.00
607	610	1.223187	AGCACCGACGGTAAAAACTG	58.777	50.000	21.25	6.63	32.11	3.16
609	612	3.876242	TTTAGCACCGACGGTAAAAAC	57.124	42.857	21.25	7.12	36.27	2.43
633	637	1.178534	CGAGCCCCACCAAACACATT	61.179	55.000	0.00	0.00	0.00	2.71
634	638	1.603455	CGAGCCCCACCAAACACAT	60.603	57.895	0.00	0.00	0.00	3.21
638	642	1.966451	CACTCGAGCCCCACCAAAC	60.966	63.158	13.61	0.00	0.00	2.93
640	644	3.636231	CCACTCGAGCCCCACCAA	61.636	66.667	13.61	0.00	0.00	3.67
641	645	4.631740	TCCACTCGAGCCCCACCA	62.632	66.667	13.61	0.00	0.00	4.17
644	648	2.060383	CATCTCCACTCGAGCCCCA	61.060	63.158	13.61	0.00	38.62	4.96
645	649	2.818132	CATCTCCACTCGAGCCCC	59.182	66.667	13.61	0.00	38.62	5.80
646	650	2.107953	GCATCTCCACTCGAGCCC	59.892	66.667	13.61	0.00	38.62	5.19
648	652	4.728058	GAGCATCTCCACTCGAGC	57.272	61.111	13.61	0.00	38.62	5.03
661	669	2.317609	GCAGCTTTCCGTTCGAGCA	61.318	57.895	0.00	0.00	38.85	4.26
663	671	1.678269	CTCGCAGCTTTCCGTTCGAG	61.678	60.000	0.00	0.00	37.65	4.04
665	673	2.772189	CTCGCAGCTTTCCGTTCG	59.228	61.111	0.00	0.00	0.00	3.95
666	674	2.476499	GCTCGCAGCTTTCCGTTC	59.524	61.111	0.00	0.00	38.45	3.95
669	677	3.112075	TTCGCTCGCAGCTTTCCG	61.112	61.111	6.58	0.00	39.60	4.30
671	679	1.886861	TTCGTTCGCTCGCAGCTTTC	61.887	55.000	6.58	0.00	39.60	2.62
673	681	2.355837	TTCGTTCGCTCGCAGCTT	60.356	55.556	6.58	0.00	39.60	3.74
706	734	0.782384	CGTTTCACTGCTCGGTACAC	59.218	55.000	0.00	0.00	0.00	2.90
800	831	2.125106	GAGTGATCCGTGGGGTGC	60.125	66.667	0.00	0.00	33.83	5.01
876	911	0.317160	GTTTTGCTTTTCGGGAGGGG	59.683	55.000	0.00	0.00	0.00	4.79
952	995	7.780822	AGGGATGGTATTAAATAGAGAGAGGA	58.219	38.462	0.00	0.00	0.00	3.71
953	996	7.125053	GGAGGGATGGTATTAAATAGAGAGAGG	59.875	44.444	0.00	0.00	0.00	3.69
954	997	7.125053	GGGAGGGATGGTATTAAATAGAGAGAG	59.875	44.444	0.00	0.00	0.00	3.20
955	998	6.960542	GGGAGGGATGGTATTAAATAGAGAGA	59.039	42.308	0.00	0.00	0.00	3.10
999	1042	2.418083	CGCTTGGAGATTTGGGGGC	61.418	63.158	0.00	0.00	0.00	5.80
1000	1043	2.418083	GCGCTTGGAGATTTGGGGG	61.418	63.158	0.00	0.00	0.00	5.40
1452	1514	4.593864	GCCCTCTCGCCACGGATC	62.594	72.222	0.00	0.00	0.00	3.36
1525	2955	2.143122	ACAGTAGCACACACATTTCCG	58.857	47.619	0.00	0.00	0.00	4.30
1544	2979	6.071503	ACAGGTACATTCTGGAACACTACTAC	60.072	42.308	0.00	0.00	36.62	2.73
1555	2990	4.389374	ACAAGAACACAGGTACATTCTGG	58.611	43.478	0.00	0.00	36.62	3.86
1564	2999	2.951642	CAACCATGACAAGAACACAGGT	59.048	45.455	0.00	0.00	32.83	4.00
1584	3046	2.035469	ATGGGGCACAACGCATCA	59.965	55.556	0.00	0.00	45.17	3.07
1657	3129	7.754027	GGAATTCAAACACAGATGAATGAGAAG	59.246	37.037	7.93	0.00	43.54	2.85
1756	3239	2.573369	CCAGGATCAAGCTCTGAATGG	58.427	52.381	1.08	7.14	37.67	3.16
1957	3557	7.837689	ACCAAGTTGTACTATCAGTATGTAGGA	59.162	37.037	1.45	0.00	37.40	2.94
1958	3558	7.921214	CACCAAGTTGTACTATCAGTATGTAGG	59.079	40.741	1.45	0.00	37.40	3.18
1959	3559	8.467598	ACACCAAGTTGTACTATCAGTATGTAG	58.532	37.037	1.45	0.00	37.40	2.74
2073	3690	3.374220	TGTTCTGGTGTGTTACGTAGG	57.626	47.619	0.00	0.00	0.00	3.18
2074	3691	3.606777	CGATGTTCTGGTGTGTTACGTAG	59.393	47.826	0.00	0.00	0.00	3.51
2075	3692	3.252944	TCGATGTTCTGGTGTGTTACGTA	59.747	43.478	0.00	0.00	0.00	3.57
2077	3694	2.661675	CTCGATGTTCTGGTGTGTTACG	59.338	50.000	0.00	0.00	0.00	3.18
2078	3695	2.993899	CCTCGATGTTCTGGTGTGTTAC	59.006	50.000	0.00	0.00	0.00	2.50
2121	3738	2.242965	ACCAGGAATGGCATGAGATTCA	59.757	45.455	0.00	0.00	31.29	2.57
2244	3894	6.476380	TCACTTCACATGCTTGAAATTTTGAC	59.524	34.615	6.60	0.00	35.07	3.18
2245	3895	6.476380	GTCACTTCACATGCTTGAAATTTTGA	59.524	34.615	6.60	0.00	35.07	2.69
2246	3896	6.292488	GGTCACTTCACATGCTTGAAATTTTG	60.292	38.462	6.60	0.00	35.07	2.44
2247	3897	5.754890	GGTCACTTCACATGCTTGAAATTTT	59.245	36.000	6.60	0.00	35.07	1.82
2249	3899	4.586001	AGGTCACTTCACATGCTTGAAATT	59.414	37.500	6.60	0.00	35.07	1.82
2251	3901	3.316029	CAGGTCACTTCACATGCTTGAAA	59.684	43.478	6.60	0.00	35.07	2.69
2253	3903	2.497138	CAGGTCACTTCACATGCTTGA	58.503	47.619	6.60	0.00	0.00	3.02
2526	4823	6.541111	AATCAAGAAAAACTGTAGTCGGAC	57.459	37.500	0.00	0.00	0.00	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.