AutoCloner

Multiple sequence alignment - TraesCS4A01G384400

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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	TraesCS4A01G384400	chr4A	100.000	2464	0	0	1	2464	662133158	662130695	0.000000e+00	4551.0
1	TraesCS4A01G384400	chr4A	96.703	546	15	2	1	546	699218186	699218728	0.000000e+00	905.0
2	TraesCS4A01G384400	chr4A	96.344	547	15	2	1	546	720592800	720592258	0.000000e+00	894.0
3	TraesCS4A01G384400	chr4A	95.238	147	7	0	1664	1810	662131348	662131202	1.470000e-57	233.0
4	TraesCS4A01G384400	chr4A	95.238	147	7	0	1811	1957	662131495	662131349	1.470000e-57	233.0
5	TraesCS4A01G384400	chr7A	92.422	1412	68	18	644	2024	260319651	260318248	0.000000e+00	1978.0
6	TraesCS4A01G384400	chr7A	96.541	318	10	1	2147	2464	260318118	260317802	2.170000e-145	525.0
7	TraesCS4A01G384400	chr7A	93.836	146	9	0	1665	1810	260318460	260318315	1.150000e-53	220.0
8	TraesCS4A01G384400	chr7A	95.238	84	1	2	2037	2117	260318194	260318111	1.990000e-26	130.0
9	TraesCS4A01G384400	chr5B	96.721	549	16	1	1	547	528060012	528060560	0.000000e+00	913.0
10	TraesCS4A01G384400	chr5B	96.007	551	17	4	1	550	637651524	637652070	0.000000e+00	891.0
11	TraesCS4A01G384400	chr5B	82.080	452	46	21	774	1206	537919577	537920012	1.080000e-93	353.0
12	TraesCS4A01G384400	chr7B	96.357	549	18	2	1	549	7444946	7444400	0.000000e+00	902.0
13	TraesCS4A01G384400	chr7B	96.337	546	18	2	1	546	665328969	665328426	0.000000e+00	896.0
14	TraesCS4A01G384400	chr7B	96.007	551	17	4	1	550	579660637	579661183	0.000000e+00	891.0
15	TraesCS4A01G384400	chr7B	88.430	121	11	3	644	763	44622460	44622342	2.550000e-30	143.0
16	TraesCS4A01G384400	chr6B	96.175	549	18	2	1	547	52962925	52962378	0.000000e+00	894.0
17	TraesCS4A01G384400	chr6B	86.310	168	20	3	1634	1800	669536190	669536025	1.950000e-41	180.0
18	TraesCS4A01G384400	chr6B	84.672	137	19	2	1811	1947	669536159	669536025	4.270000e-28	135.0
19	TraesCS4A01G384400	chr6B	73.737	198	47	5	2040	2234	713405926	713406121	3.400000e-09	73.1
20	TraesCS4A01G384400	chr6B	100.000	28	0	0	2069	2096	709007759	709007786	4.000000e-03	52.8
21	TraesCS4A01G384400	chr4B	96.337	546	16	1	1	546	672456407	672456948	0.000000e+00	894.0
22	TraesCS4A01G384400	chr2A	96.350	411	15	0	1623	2033	12351797	12352207	0.000000e+00	676.0
23	TraesCS4A01G384400	chr2A	92.927	410	15	2	641	1037	12345957	12346365	3.530000e-163	584.0
24	TraesCS4A01G384400	chr2A	95.710	303	11	2	2037	2338	12352244	12352545	1.020000e-133	486.0
25	TraesCS4A01G384400	chr2A	91.030	301	14	5	1100	1388	12346364	12346663	6.390000e-106	394.0
26	TraesCS4A01G384400	chr2A	91.758	182	10	3	1392	1573	12351624	12351800	5.260000e-62	248.0
27	TraesCS4A01G384400	chr2A	95.918	147	6	0	1664	1810	12351985	12352131	3.170000e-59	239.0
28	TraesCS4A01G384400	chr2A	95.420	131	6	0	2334	2464	12357361	12357491	2.480000e-50	209.0
29	TraesCS4A01G384400	chr2A	94.898	98	5	0	547	644	729828963	729829060	1.180000e-33	154.0
30	TraesCS4A01G384400	chr2B	88.714	381	37	6	2074	2454	770437141	770436767	6.210000e-126	460.0
31	TraesCS4A01G384400	chr7D	91.613	310	23	3	2074	2383	212818961	212818655	2.260000e-115	425.0
32	TraesCS4A01G384400	chr3B	88.319	351	28	8	2074	2424	696583903	696583566	2.280000e-110	409.0
33	TraesCS4A01G384400	chr3B	90.476	42	3	1	2056	2096	750876087	750876128	1.000000e-03	54.7
34	TraesCS4A01G384400	chrUn	91.986	287	18	5	2168	2454	60537164	60537445	4.940000e-107	398.0
35	TraesCS4A01G384400	chrUn	94.118	51	3	0	2071	2121	60537120	60537170	7.310000e-11	78.7
36	TraesCS4A01G384400	chr4D	80.930	430	70	10	2040	2463	50982116	50981693	1.830000e-86	329.0
37	TraesCS4A01G384400	chr1A	75.117	426	102	3	2041	2464	335553887	335553464	1.930000e-46	196.0
38	TraesCS4A01G384400	chr5A	85.455	165	21	3	1634	1797	611013065	611013227	4.210000e-38	169.0
39	TraesCS4A01G384400	chr5A	79.339	242	28	7	1811	2032	611013096	611013335	1.530000e-32	150.0
40	TraesCS4A01G384400	chr3D	84.242	165	24	2	1634	1797	1692355	1692518	2.540000e-35	159.0
41	TraesCS4A01G384400	chr3D	78.261	230	30	5	1823	2032	1692397	1692626	1.990000e-26	130.0

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	TraesCS4A01G384400	chr4A	662130695	662133158	2463	True	1672.333333	4551	96.825333	1	2464	3	chr4A.!!$R2	2463
1	TraesCS4A01G384400	chr4A	699218186	699218728	542	False	905.000000	905	96.703000	1	546	1	chr4A.!!$F1	545
2	TraesCS4A01G384400	chr4A	720592258	720592800	542	True	894.000000	894	96.344000	1	546	1	chr4A.!!$R1	545
3	TraesCS4A01G384400	chr7A	260317802	260319651	1849	True	713.250000	1978	94.509250	644	2464	4	chr7A.!!$R1	1820
4	TraesCS4A01G384400	chr5B	528060012	528060560	548	False	913.000000	913	96.721000	1	547	1	chr5B.!!$F1	546
5	TraesCS4A01G384400	chr5B	637651524	637652070	546	False	891.000000	891	96.007000	1	550	1	chr5B.!!$F3	549
6	TraesCS4A01G384400	chr7B	7444400	7444946	546	True	902.000000	902	96.357000	1	549	1	chr7B.!!$R1	548
7	TraesCS4A01G384400	chr7B	665328426	665328969	543	True	896.000000	896	96.337000	1	546	1	chr7B.!!$R3	545
8	TraesCS4A01G384400	chr7B	579660637	579661183	546	False	891.000000	891	96.007000	1	550	1	chr7B.!!$F1	549
9	TraesCS4A01G384400	chr6B	52962378	52962925	547	True	894.000000	894	96.175000	1	547	1	chr6B.!!$R1	546
10	TraesCS4A01G384400	chr4B	672456407	672456948	541	False	894.000000	894	96.337000	1	546	1	chr4B.!!$F1	545
11	TraesCS4A01G384400	chr2A	12345957	12346663	706	False	489.000000	584	91.978500	641	1388	2	chr2A.!!$F3	747
12	TraesCS4A01G384400	chr2A	12351624	12352545	921	False	412.250000	676	94.934000	1392	2338	4	chr2A.!!$F4	946

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
699	709	0.104304	GGTATCGCCAACCATCGACT	59.896	55.0	0.0	0.0	37.55	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2385	2476	1.349688	AGCATGACGGTCTGGGTTTAA	59.65	47.619	9.88	0.0	0.0	1.52	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
74	77	4.451900	ACTTGTTGTTCGACCAATCTCTT	58.548	39.130	0.00	0.00	0.00	2.85
207	210	3.444034	CGGACATAAGAGAGGACACTTCA	59.556	47.826	0.00	0.00	0.00	3.02
246	249	8.826710	GCTAGCTAACACAATATATGAAACACA	58.173	33.333	7.70	0.00	0.00	3.72
326	336	1.763120	AGCCACTGGAATGCTGACA	59.237	52.632	0.00	0.00	33.23	3.58
335	345	1.675714	GGAATGCTGACACGTGGATGA	60.676	52.381	21.57	0.00	0.00	2.92
489	499	2.613474	CGACCCATTAGTTCCGGTTCAA	60.613	50.000	0.00	0.00	0.00	2.69
549	559	5.224821	AGGTGTTTTTCTACTAGTGGTCC	57.775	43.478	5.39	0.00	0.00	4.46
550	560	4.906060	AGGTGTTTTTCTACTAGTGGTCCT	59.094	41.667	5.39	1.82	0.00	3.85
551	561	5.368816	AGGTGTTTTTCTACTAGTGGTCCTT	59.631	40.000	5.39	0.00	0.00	3.36
552	562	5.469084	GGTGTTTTTCTACTAGTGGTCCTTG	59.531	44.000	5.39	0.00	0.00	3.61
553	563	6.053650	GTGTTTTTCTACTAGTGGTCCTTGT	58.946	40.000	5.39	0.00	33.57	3.16
554	564	6.541278	GTGTTTTTCTACTAGTGGTCCTTGTT	59.459	38.462	5.39	0.00	31.40	2.83
555	565	7.066645	GTGTTTTTCTACTAGTGGTCCTTGTTT	59.933	37.037	5.39	0.00	31.40	2.83
556	566	7.066525	TGTTTTTCTACTAGTGGTCCTTGTTTG	59.933	37.037	5.39	0.00	31.40	2.93
557	567	4.884668	TCTACTAGTGGTCCTTGTTTGG	57.115	45.455	5.39	0.00	31.40	3.28
558	568	4.228824	TCTACTAGTGGTCCTTGTTTGGT	58.771	43.478	5.39	0.00	31.40	3.67
559	569	5.396485	TCTACTAGTGGTCCTTGTTTGGTA	58.604	41.667	5.39	0.00	31.40	3.25
560	570	5.840149	TCTACTAGTGGTCCTTGTTTGGTAA	59.160	40.000	5.39	0.00	31.40	2.85
561	571	5.578157	ACTAGTGGTCCTTGTTTGGTAAT	57.422	39.130	0.00	0.00	0.00	1.89
562	572	5.557866	ACTAGTGGTCCTTGTTTGGTAATC	58.442	41.667	0.00	0.00	0.00	1.75
563	573	3.408634	AGTGGTCCTTGTTTGGTAATCG	58.591	45.455	0.00	0.00	0.00	3.34
564	574	2.486592	GTGGTCCTTGTTTGGTAATCGG	59.513	50.000	0.00	0.00	0.00	4.18
565	575	2.372504	TGGTCCTTGTTTGGTAATCGGA	59.627	45.455	0.00	0.00	0.00	4.55
566	576	3.007635	GGTCCTTGTTTGGTAATCGGAG	58.992	50.000	0.00	0.00	0.00	4.63
567	577	3.007635	GTCCTTGTTTGGTAATCGGAGG	58.992	50.000	0.00	0.00	0.00	4.30
568	578	2.907696	TCCTTGTTTGGTAATCGGAGGA	59.092	45.455	0.00	0.00	0.00	3.71
569	579	3.007635	CCTTGTTTGGTAATCGGAGGAC	58.992	50.000	0.00	0.00	0.00	3.85
570	580	2.373540	TGTTTGGTAATCGGAGGACG	57.626	50.000	0.00	0.00	46.11	4.79
571	581	1.619827	TGTTTGGTAATCGGAGGACGT	59.380	47.619	0.00	0.00	44.69	4.34
572	582	2.265683	GTTTGGTAATCGGAGGACGTC	58.734	52.381	7.13	7.13	44.69	4.34
573	583	0.819582	TTGGTAATCGGAGGACGTCC	59.180	55.000	27.67	27.67	44.69	4.79
580	590	3.721868	GGAGGACGTCCAATGGGA	58.278	61.111	35.00	0.00	46.10	4.37
598	608	1.698506	GATGAGGGATCCACGAGTCT	58.301	55.000	15.23	0.00	0.00	3.24
599	609	1.611491	GATGAGGGATCCACGAGTCTC	59.389	57.143	15.23	10.12	0.00	3.36
600	610	0.626382	TGAGGGATCCACGAGTCTCT	59.374	55.000	15.23	0.00	0.00	3.10
601	611	1.314730	GAGGGATCCACGAGTCTCTC	58.685	60.000	15.23	4.35	35.04	3.20
602	612	0.106419	AGGGATCCACGAGTCTCTCC	60.106	60.000	15.23	0.00	0.00	3.71
603	613	0.395862	GGGATCCACGAGTCTCTCCA	60.396	60.000	15.23	0.00	0.00	3.86
604	614	1.698506	GGATCCACGAGTCTCTCCAT	58.301	55.000	6.95	0.00	0.00	3.41
605	615	2.489255	GGGATCCACGAGTCTCTCCATA	60.489	54.545	15.23	0.00	0.00	2.74
606	616	3.426615	GGATCCACGAGTCTCTCCATAT	58.573	50.000	6.95	0.00	0.00	1.78
607	617	3.192422	GGATCCACGAGTCTCTCCATATG	59.808	52.174	6.95	0.00	0.00	1.78
608	618	3.298686	TCCACGAGTCTCTCCATATGT	57.701	47.619	1.24	0.00	0.00	2.29
609	619	2.952310	TCCACGAGTCTCTCCATATGTG	59.048	50.000	1.24	0.00	0.00	3.21
622	632	2.934887	CATATGTGGACTGATTGCCCA	58.065	47.619	0.00	0.00	0.00	5.36
623	633	3.493334	CATATGTGGACTGATTGCCCAT	58.507	45.455	0.00	0.00	31.94	4.00
624	634	2.537633	ATGTGGACTGATTGCCCATT	57.462	45.000	0.00	0.00	31.94	3.16
625	635	3.668141	ATGTGGACTGATTGCCCATTA	57.332	42.857	0.00	0.00	31.94	1.90
626	636	2.722094	TGTGGACTGATTGCCCATTAC	58.278	47.619	0.00	0.00	31.94	1.89
627	637	2.024414	GTGGACTGATTGCCCATTACC	58.976	52.381	0.00	0.00	31.94	2.85
628	638	1.638070	TGGACTGATTGCCCATTACCA	59.362	47.619	0.00	0.00	0.00	3.25
629	639	2.042297	TGGACTGATTGCCCATTACCAA	59.958	45.455	0.00	0.00	0.00	3.67
630	640	3.299503	GGACTGATTGCCCATTACCAAT	58.700	45.455	0.00	0.00	34.57	3.16
631	641	4.079500	TGGACTGATTGCCCATTACCAATA	60.080	41.667	0.00	0.00	32.20	1.90
632	642	4.278419	GGACTGATTGCCCATTACCAATAC	59.722	45.833	0.00	0.00	32.20	1.89
633	643	3.882888	ACTGATTGCCCATTACCAATACG	59.117	43.478	0.00	0.00	32.20	3.06
634	644	2.621055	TGATTGCCCATTACCAATACGC	59.379	45.455	0.00	0.00	32.20	4.42
635	645	1.394618	TTGCCCATTACCAATACGCC	58.605	50.000	0.00	0.00	0.00	5.68
636	646	0.256177	TGCCCATTACCAATACGCCA	59.744	50.000	0.00	0.00	0.00	5.69
637	647	0.951558	GCCCATTACCAATACGCCAG	59.048	55.000	0.00	0.00	0.00	4.85
638	648	1.476110	GCCCATTACCAATACGCCAGA	60.476	52.381	0.00	0.00	0.00	3.86
639	649	2.814097	GCCCATTACCAATACGCCAGAT	60.814	50.000	0.00	0.00	0.00	2.90
640	650	3.074412	CCCATTACCAATACGCCAGATC	58.926	50.000	0.00	0.00	0.00	2.75
641	651	3.495983	CCCATTACCAATACGCCAGATCA	60.496	47.826	0.00	0.00	0.00	2.92
642	652	3.748048	CCATTACCAATACGCCAGATCAG	59.252	47.826	0.00	0.00	0.00	2.90
698	708	0.179094	TGGTATCGCCAACCATCGAC	60.179	55.000	0.00	0.00	45.94	4.20
699	709	0.104304	GGTATCGCCAACCATCGACT	59.896	55.000	0.00	0.00	37.55	4.18
704	714	0.165944	CGCCAACCATCGACTTTGTC	59.834	55.000	0.00	0.00	0.00	3.18
719	729	1.434513	TTGTCTTGGGGATGTGGGCT	61.435	55.000	0.00	0.00	0.00	5.19
835	846	1.003118	TCACATGGTGGAAGTAGTGCC	59.997	52.381	0.00	0.00	33.87	5.01
868	879	6.269077	TCCAGCGAGGTCATTTATTATCCTAA	59.731	38.462	0.00	0.00	39.02	2.69
1001	1025	1.078426	GCGGCAGGTTAGTGGTGAT	60.078	57.895	0.00	0.00	0.00	3.06
1010	1034	1.389106	GTTAGTGGTGATGTTCGTCGC	59.611	52.381	0.00	0.00	0.00	5.19
1058	1082	3.667261	CGGTTCTACAACTACAAGTGTCG	59.333	47.826	0.00	0.00	32.50	4.35
1068	1092	4.065088	ACTACAAGTGTCGCAATCACAAT	58.935	39.130	5.87	0.00	38.16	2.71
1071	1095	3.812609	ACAAGTGTCGCAATCACAATGTA	59.187	39.130	10.27	0.00	36.83	2.29
1102	1126	2.201732	TGAGTCAACGAGTGTTTGCTC	58.798	47.619	0.00	0.00	35.72	4.26
1103	1127	2.159099	TGAGTCAACGAGTGTTTGCTCT	60.159	45.455	0.00	0.00	37.27	4.09
1224	1248	1.221840	CACCTGGCTACGCTTGGAT	59.778	57.895	0.00	0.00	0.00	3.41
1231	1267	0.384669	GCTACGCTTGGATCGGTAGT	59.615	55.000	0.00	0.00	0.00	2.73
1242	1278	3.627123	TGGATCGGTAGTGCAAATCAATG	59.373	43.478	0.00	0.00	0.00	2.82
1397	1445	4.873810	ACTGTGGCGGCTGTTGCA	62.874	61.111	11.43	0.76	41.91	4.08
1433	1481	4.899239	GCCCTCGACCCTGCATCG	62.899	72.222	1.75	1.75	41.00	3.84
1588	1637	5.176406	CCAATAGTAGAACATGTCATCAGCG	59.824	44.000	0.00	0.00	0.00	5.18
1786	1835	5.534654	TCATACAAGGGAAAAACAGTGGAAG	59.465	40.000	0.00	0.00	0.00	3.46
1843	1892	9.892130	AAGGTTTTAGACATATACAAGAGGAAG	57.108	33.333	0.00	0.00	0.00	3.46
1861	1910	6.373774	AGAGGAAGCATTGTCACAATTTCTAG	59.626	38.462	12.61	0.00	0.00	2.43
1976	2025	1.194547	CACATTTCCACAGGTCGTTCG	59.805	52.381	0.00	0.00	0.00	3.95
2115	2206	1.135333	TGGTTCGCGACATATACTGCA	59.865	47.619	9.15	0.00	0.00	4.41
2121	2212	2.857748	CGCGACATATACTGCAGAAACA	59.142	45.455	23.35	2.41	0.00	2.83
2126	2217	6.019075	GCGACATATACTGCAGAAACATGTTA	60.019	38.462	23.35	0.00	0.00	2.41
2178	2269	6.344500	CATCTAGATGTGCCAGAAACTTACT	58.656	40.000	22.42	0.00	34.23	2.24
2299	2390	2.881513	TGAAATTTCCAACTGCGCTACA	59.118	40.909	15.48	0.00	0.00	2.74
2319	2410	2.184830	CCAGCATCACTCCCGCATG	61.185	63.158	0.00	0.00	0.00	4.06
2378	2469	5.234972	CCTTTTGGCTTGTTGAACTCAATTC	59.765	40.000	0.00	0.00	38.24	2.17
2385	2476	5.807011	GCTTGTTGAACTCAATTCTGTGTTT	59.193	36.000	0.00	0.00	38.92	2.83

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
74	77	1.747552	CGATCGACCTCTCCTTCTCCA	60.748	57.143	10.26	0.00	0.00	3.86
335	345	1.616159	CACCAATCGGGACCAAAAGT	58.384	50.000	0.00	0.00	41.15	2.66
489	499	1.559965	GGGCCTTTAGTCCCGGTTCT	61.560	60.000	0.84	0.15	32.00	3.01
549	559	2.671396	CGTCCTCCGATTACCAAACAAG	59.329	50.000	0.00	0.00	39.56	3.16
550	560	2.037511	ACGTCCTCCGATTACCAAACAA	59.962	45.455	0.00	0.00	40.70	2.83
551	561	1.619827	ACGTCCTCCGATTACCAAACA	59.380	47.619	0.00	0.00	40.70	2.83
552	562	2.265683	GACGTCCTCCGATTACCAAAC	58.734	52.381	3.51	0.00	40.70	2.93
553	563	1.205417	GGACGTCCTCCGATTACCAAA	59.795	52.381	27.64	0.00	40.70	3.28
554	564	0.819582	GGACGTCCTCCGATTACCAA	59.180	55.000	27.64	0.00	40.70	3.67
555	565	0.323633	TGGACGTCCTCCGATTACCA	60.324	55.000	33.39	8.70	43.03	3.25
556	566	0.819582	TTGGACGTCCTCCGATTACC	59.180	55.000	33.39	5.88	43.03	2.85
557	567	2.470821	CATTGGACGTCCTCCGATTAC	58.529	52.381	33.39	5.94	40.00	1.89
558	568	1.411246	CCATTGGACGTCCTCCGATTA	59.589	52.381	33.39	10.38	40.00	1.75
559	569	0.178068	CCATTGGACGTCCTCCGATT	59.822	55.000	33.39	8.56	40.00	3.34
560	570	1.686325	CCCATTGGACGTCCTCCGAT	61.686	60.000	33.39	19.05	43.46	4.18
561	571	2.355986	CCCATTGGACGTCCTCCGA	61.356	63.158	33.39	17.72	43.03	4.55
562	572	1.686325	ATCCCATTGGACGTCCTCCG	61.686	60.000	33.39	20.71	45.58	4.63
563	573	0.179045	CATCCCATTGGACGTCCTCC	60.179	60.000	33.39	10.65	45.58	4.30
564	574	0.830648	TCATCCCATTGGACGTCCTC	59.169	55.000	33.39	10.53	45.58	3.71
565	575	0.833287	CTCATCCCATTGGACGTCCT	59.167	55.000	33.39	13.58	45.58	3.85
566	576	0.179045	CCTCATCCCATTGGACGTCC	60.179	60.000	28.17	28.17	45.58	4.79
567	577	0.179045	CCCTCATCCCATTGGACGTC	60.179	60.000	7.13	7.13	45.58	4.34
568	578	0.620410	TCCCTCATCCCATTGGACGT	60.620	55.000	3.62	0.00	45.58	4.34
569	579	0.767375	ATCCCTCATCCCATTGGACG	59.233	55.000	3.62	0.00	45.58	4.79
570	580	1.074566	GGATCCCTCATCCCATTGGAC	59.925	57.143	3.62	0.00	45.33	4.02
571	581	1.449271	GGATCCCTCATCCCATTGGA	58.551	55.000	3.62	0.00	45.33	3.53
579	589	1.611491	GAGACTCGTGGATCCCTCATC	59.389	57.143	9.90	0.58	0.00	2.92
580	590	1.216678	AGAGACTCGTGGATCCCTCAT	59.783	52.381	9.90	0.00	0.00	2.90
581	591	0.626382	AGAGACTCGTGGATCCCTCA	59.374	55.000	9.90	0.00	0.00	3.86
582	592	1.314730	GAGAGACTCGTGGATCCCTC	58.685	60.000	9.90	7.31	0.00	4.30
583	593	0.106419	GGAGAGACTCGTGGATCCCT	60.106	60.000	9.90	0.00	0.00	4.20
584	594	0.395862	TGGAGAGACTCGTGGATCCC	60.396	60.000	9.90	0.00	0.00	3.85
585	595	1.698506	ATGGAGAGACTCGTGGATCC	58.301	55.000	4.20	4.20	0.00	3.36
586	596	3.823873	ACATATGGAGAGACTCGTGGATC	59.176	47.826	7.80	0.00	0.00	3.36
587	597	3.571828	CACATATGGAGAGACTCGTGGAT	59.428	47.826	7.80	0.00	0.00	3.41
588	598	2.952310	CACATATGGAGAGACTCGTGGA	59.048	50.000	7.80	0.00	0.00	4.02
589	599	3.361794	CACATATGGAGAGACTCGTGG	57.638	52.381	7.80	0.00	0.00	4.94
609	619	2.435372	TGGTAATGGGCAATCAGTCC	57.565	50.000	0.00	0.00	44.53	3.85
610	620	4.024048	CGTATTGGTAATGGGCAATCAGTC	60.024	45.833	0.00	0.00	0.00	3.51
611	621	3.882888	CGTATTGGTAATGGGCAATCAGT	59.117	43.478	0.00	0.00	0.00	3.41
612	622	3.304659	GCGTATTGGTAATGGGCAATCAG	60.305	47.826	0.00	0.00	0.00	2.90
613	623	2.621055	GCGTATTGGTAATGGGCAATCA	59.379	45.455	0.00	0.00	0.00	2.57
614	624	2.030274	GGCGTATTGGTAATGGGCAATC	60.030	50.000	0.00	0.00	0.00	2.67
615	625	1.960689	GGCGTATTGGTAATGGGCAAT	59.039	47.619	0.00	0.00	0.00	3.56
616	626	1.341089	TGGCGTATTGGTAATGGGCAA	60.341	47.619	0.00	0.00	31.62	4.52
617	627	0.256177	TGGCGTATTGGTAATGGGCA	59.744	50.000	0.00	0.00	0.00	5.36
618	628	0.951558	CTGGCGTATTGGTAATGGGC	59.048	55.000	0.00	0.00	0.00	5.36
619	629	2.631160	TCTGGCGTATTGGTAATGGG	57.369	50.000	0.00	0.00	0.00	4.00
620	630	3.738982	TGATCTGGCGTATTGGTAATGG	58.261	45.455	0.00	0.00	0.00	3.16
621	631	3.187227	GCTGATCTGGCGTATTGGTAATG	59.813	47.826	1.46	0.00	0.00	1.90
622	632	3.403038	GCTGATCTGGCGTATTGGTAAT	58.597	45.455	1.46	0.00	0.00	1.89
623	633	2.801699	CGCTGATCTGGCGTATTGGTAA	60.802	50.000	19.87	0.00	46.37	2.85
624	634	1.269569	CGCTGATCTGGCGTATTGGTA	60.270	52.381	19.87	0.00	46.37	3.25
625	635	0.530650	CGCTGATCTGGCGTATTGGT	60.531	55.000	19.87	0.00	46.37	3.67
626	636	2.229039	CGCTGATCTGGCGTATTGG	58.771	57.895	19.87	0.00	46.37	3.16
633	643	1.474077	ACCAATTTTCGCTGATCTGGC	59.526	47.619	1.46	1.75	0.00	4.85
634	644	3.504863	CAACCAATTTTCGCTGATCTGG	58.495	45.455	1.46	0.00	0.00	3.86
635	645	3.504863	CCAACCAATTTTCGCTGATCTG	58.495	45.455	0.00	0.00	0.00	2.90
636	646	2.094545	GCCAACCAATTTTCGCTGATCT	60.095	45.455	0.00	0.00	0.00	2.75
637	647	2.262211	GCCAACCAATTTTCGCTGATC	58.738	47.619	0.00	0.00	0.00	2.92
638	648	1.402720	CGCCAACCAATTTTCGCTGAT	60.403	47.619	0.00	0.00	0.00	2.90
639	649	0.039617	CGCCAACCAATTTTCGCTGA	60.040	50.000	0.00	0.00	0.00	4.26
640	650	0.318614	ACGCCAACCAATTTTCGCTG	60.319	50.000	0.00	0.00	0.00	5.18
641	651	0.318614	CACGCCAACCAATTTTCGCT	60.319	50.000	0.00	0.00	0.00	4.93
642	652	1.281566	CCACGCCAACCAATTTTCGC	61.282	55.000	0.00	0.00	0.00	4.70
698	708	1.549203	CCCACATCCCCAAGACAAAG	58.451	55.000	0.00	0.00	0.00	2.77
699	709	0.541764	GCCCACATCCCCAAGACAAA	60.542	55.000	0.00	0.00	0.00	2.83
704	714	0.394352	GTACAGCCCACATCCCCAAG	60.394	60.000	0.00	0.00	0.00	3.61
719	729	4.279169	ACAAGACCTAAAGTACAGCGTACA	59.721	41.667	17.11	1.31	0.00	2.90
765	776	0.900647	AGGACCAGACGGAGACCAAG	60.901	60.000	0.00	0.00	35.59	3.61
868	879	1.205460	AGATGGGTTGCGGGGTAAGT	61.205	55.000	0.00	0.00	0.00	2.24
1010	1034	3.147294	CGAACTGACCACGCTTCG	58.853	61.111	0.00	0.00	0.00	3.79
1058	1082	6.199937	AGATCCACTTTACATTGTGATTGC	57.800	37.500	0.00	0.00	36.38	3.56
1068	1092	4.988540	CGTTGACTCAAGATCCACTTTACA	59.011	41.667	0.00	0.00	36.61	2.41
1071	1095	4.202264	ACTCGTTGACTCAAGATCCACTTT	60.202	41.667	0.00	0.00	36.61	2.66
1224	1248	3.689161	CCTTCATTGATTTGCACTACCGA	59.311	43.478	0.00	0.00	0.00	4.69
1231	1267	2.892215	TGCTGACCTTCATTGATTTGCA	59.108	40.909	0.00	0.00	0.00	4.08
1242	1278	0.729690	GCGATTTCCTGCTGACCTTC	59.270	55.000	0.00	0.00	0.00	3.46
1380	1428	4.873810	TGCAACAGCCGCCACAGT	62.874	61.111	0.00	0.00	0.00	3.55
1397	1445	1.028330	CGATGGTTGCCTGATGCTGT	61.028	55.000	0.00	0.00	42.00	4.40
1433	1481	4.549458	CAACAGACACCACCAAATTGATC	58.451	43.478	0.00	0.00	0.00	2.92
1588	1637	4.764679	TCTCATGTTATTTGTGTGTGCC	57.235	40.909	0.00	0.00	0.00	5.01
1742	1791	8.414003	TGTATGATTCTTGCTTACTACCTAGTG	58.586	37.037	0.00	0.00	37.10	2.74
1743	1792	8.534954	TGTATGATTCTTGCTTACTACCTAGT	57.465	34.615	0.00	0.00	40.24	2.57
1746	1795	7.275920	CCTTGTATGATTCTTGCTTACTACCT	58.724	38.462	0.00	0.00	0.00	3.08
1751	1800	7.391148	TTTCCCTTGTATGATTCTTGCTTAC	57.609	36.000	0.00	0.00	0.00	2.34
1753	1802	6.916360	TTTTCCCTTGTATGATTCTTGCTT	57.084	33.333	0.00	0.00	0.00	3.91
1758	1807	6.209391	CCACTGTTTTTCCCTTGTATGATTCT	59.791	38.462	0.00	0.00	0.00	2.40
1759	1808	6.208599	TCCACTGTTTTTCCCTTGTATGATTC	59.791	38.462	0.00	0.00	0.00	2.52
1760	1809	6.074648	TCCACTGTTTTTCCCTTGTATGATT	58.925	36.000	0.00	0.00	0.00	2.57
1786	1835	9.817809	TTAGATTAATCTGGTGTATCACTGAAC	57.182	33.333	25.22	0.00	37.76	3.18
1843	1892	4.156556	TCAGCCTAGAAATTGTGACAATGC	59.843	41.667	12.09	9.52	0.00	3.56
1907	1956	6.074648	TCCACTGTTTTTCCCTTGTATGATT	58.925	36.000	0.00	0.00	0.00	2.57
1976	2025	3.728845	TGTTCCTCAGAAAGCTACACAC	58.271	45.455	0.00	0.00	32.58	3.82
2115	2206	6.320164	TGGTACAAGCAAACTAACATGTTTCT	59.680	34.615	17.78	0.00	34.74	2.52
2121	2212	5.183140	GGATGTGGTACAAGCAAACTAACAT	59.817	40.000	0.00	0.00	44.16	2.71
2126	2217	3.508845	AGGATGTGGTACAAGCAAACT	57.491	42.857	0.00	0.00	44.16	2.66
2299	2390	1.703014	ATGCGGGAGTGATGCTGGAT	61.703	55.000	0.00	0.00	0.00	3.41
2319	2410	3.186909	GTGTTCCTGAACCACAAAAAGC	58.813	45.455	7.51	0.00	40.46	3.51
2385	2476	1.349688	AGCATGACGGTCTGGGTTTAA	59.650	47.619	9.88	0.00	0.00	1.52
2420	2511	9.534565	TCTTAGATCAGCAATGTATAAACTGAC	57.465	33.333	0.00	0.00	39.97	3.51

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.