AutoCloner

Multiple sequence alignment - TraesCS1A01G185700

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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	TraesCS1A01G185700	chr1A	100.000	2747	0	0	1	2747	336475094	336477840	0.000000e+00	5073.0
1	TraesCS1A01G185700	chr1A	95.185	270	13	0	397	666	336470276	336470545	7.030000e-116	427.0
2	TraesCS1A01G185700	chr1D	91.473	1337	52	14	663	1945	262474586	262475914	0.000000e+00	1781.0
3	TraesCS1A01G185700	chr1D	90.812	751	31	15	2003	2747	262476037	262476755	0.000000e+00	970.0
4	TraesCS1A01G185700	chr1D	81.001	679	93	32	6	666	68658333	68657673	8.780000e-140	507.0
5	TraesCS1A01G185700	chr1D	100.000	28	0	0	2379	2406	162348739	162348712	5.000000e-03	52.8
6	TraesCS1A01G185700	chr1B	88.536	1291	64	29	896	2134	348478632	348479890	0.000000e+00	1487.0
7	TraesCS1A01G185700	chr1B	90.717	237	7	3	663	899	348474855	348475076	4.450000e-78	302.0
8	TraesCS1A01G185700	chr1B	92.126	127	10	0	2621	2747	348480764	348480890	2.170000e-41	180.0
9	TraesCS1A01G185700	chr1B	95.238	42	2	0	1938	1979	636878999	636878958	1.770000e-07	67.6
10	TraesCS1A01G185700	chr2A	94.745	666	35	0	1	666	683219009	683219674	0.000000e+00	1037.0
11	TraesCS1A01G185700	chr2A	89.796	49	4	1	1931	1979	28818860	28818813	8.210000e-06	62.1
12	TraesCS1A01G185700	chr2B	93.939	396	23	1	1	395	767167133	767167528	5.060000e-167	597.0
13	TraesCS1A01G185700	chr2B	90.809	272	21	3	398	666	767153816	767154086	7.230000e-96	361.0
14	TraesCS1A01G185700	chr2B	94.286	35	2	0	2372	2406	89705362	89705396	1.000000e-03	54.7
15	TraesCS1A01G185700	chr7D	85.849	530	61	13	3	522	628706010	628706535	4.000000e-153	551.0
16	TraesCS1A01G185700	chr7D	85.799	507	58	11	3	498	506153930	506154433	2.420000e-145	525.0
17	TraesCS1A01G185700	chr3B	84.848	528	65	14	3	522	219337629	219338149	4.060000e-143	518.0
18	TraesCS1A01G185700	chr3B	84.848	528	65	14	3	522	220625170	220625690	4.060000e-143	518.0
19	TraesCS1A01G185700	chr3B	100.000	32	0	0	2423	2454	777346590	777346559	2.950000e-05	60.2
20	TraesCS1A01G185700	chr7A	84.688	529	66	14	3	522	688984112	688983590	5.250000e-142	514.0
21	TraesCS1A01G185700	chr7A	88.679	53	5	1	1935	1986	1755737	1755789	2.280000e-06	63.9
22	TraesCS1A01G185700	chr6D	80.265	679	96	32	6	666	193219372	193218714	6.880000e-131	477.0
23	TraesCS1A01G185700	chr6D	86.207	58	6	2	1924	1979	88104751	88104694	8.210000e-06	62.1
24	TraesCS1A01G185700	chr6D	100.000	29	0	0	2383	2411	335365773	335365801	1.000000e-03	54.7
25	TraesCS1A01G185700	chr5A	81.961	255	26	15	1350	1594	661149077	661148833	6.000000e-47	198.0
26	TraesCS1A01G185700	chr5A	90.000	50	3	2	1931	1979	558168928	558168880	2.280000e-06	63.9
27	TraesCS1A01G185700	chr5A	100.000	28	0	0	2379	2406	347544181	347544208	5.000000e-03	52.8
28	TraesCS1A01G185700	chr5A	100.000	28	0	0	2379	2406	347544325	347544298	5.000000e-03	52.8
29	TraesCS1A01G185700	chr4D	87.654	162	20	0	1351	1512	481548011	481548172	3.610000e-44	189.0
30	TraesCS1A01G185700	chr4D	100.000	29	0	0	2384	2412	477041040	477041012	1.000000e-03	54.7
31	TraesCS1A01G185700	chr2D	100.000	39	0	0	1937	1975	639902307	639902269	3.790000e-09	73.1
32	TraesCS1A01G185700	chr4B	91.837	49	2	2	1936	1982	526954610	526954562	1.770000e-07	67.6
33	TraesCS1A01G185700	chr4B	94.737	38	2	0	2424	2461	589806890	589806853	2.950000e-05	60.2
34	TraesCS1A01G185700	chr5D	93.333	45	2	1	1933	1976	201803137	201803181	6.350000e-07	65.8
35	TraesCS1A01G185700	chrUn	88.679	53	5	1	1935	1986	284001405	284001353	2.280000e-06	63.9
36	TraesCS1A01G185700	chrUn	96.970	33	1	0	2379	2411	110340459	110340491	3.820000e-04	56.5

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	TraesCS1A01G185700	chr1A	336475094	336477840	2746	False	5073.000000	5073	100.000000	1	2747	1	chr1A.!!$F2	2746
1	TraesCS1A01G185700	chr1D	262474586	262476755	2169	False	1375.500000	1781	91.142500	663	2747	2	chr1D.!!$F1	2084
2	TraesCS1A01G185700	chr1D	68657673	68658333	660	True	507.000000	507	81.001000	6	666	1	chr1D.!!$R1	660
3	TraesCS1A01G185700	chr1B	348474855	348480890	6035	False	656.333333	1487	90.459667	663	2747	3	chr1B.!!$F1	2084
4	TraesCS1A01G185700	chr2A	683219009	683219674	665	False	1037.000000	1037	94.745000	1	666	1	chr2A.!!$F1	665
5	TraesCS1A01G185700	chr7D	628706010	628706535	525	False	551.000000	551	85.849000	3	522	1	chr7D.!!$F2	519
6	TraesCS1A01G185700	chr7D	506153930	506154433	503	False	525.000000	525	85.799000	3	498	1	chr7D.!!$F1	495
7	TraesCS1A01G185700	chr3B	219337629	219338149	520	False	518.000000	518	84.848000	3	522	1	chr3B.!!$F1	519
8	TraesCS1A01G185700	chr3B	220625170	220625690	520	False	518.000000	518	84.848000	3	522	1	chr3B.!!$F2	519
9	TraesCS1A01G185700	chr7A	688983590	688984112	522	True	514.000000	514	84.688000	3	522	1	chr7A.!!$R1	519
10	TraesCS1A01G185700	chr6D	193218714	193219372	658	True	477.000000	477	80.265000	6	666	1	chr6D.!!$R2	660

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
640	689	0.041833	TAGGCTGCTCTCCTCACCTT	59.958	55.0	0.0	0.0	35.21	3.5	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2389	6128	0.109723	TTGTTTTGGGACGGAGGGAG	59.89	55.0	0.0	0.0	0.0	4.3	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
236	237	2.355837	GCTTGGACAGCGTCGTGA	60.356	61.111	0.00	0.00	39.29	4.35
242	243	2.910479	ACAGCGTCGTGACTCCCA	60.910	61.111	0.00	0.00	0.00	4.37
250	251	1.972223	CGTGACTCCCACTCCGAGT	60.972	63.158	0.00	0.00	43.53	4.18
323	324	2.356022	CCTGATGCAGTGGATGTTACCA	60.356	50.000	0.12	0.00	37.63	3.25
419	424	1.340308	TGACGACCGATGAACCCTAGA	60.340	52.381	0.00	0.00	0.00	2.43
475	506	2.445654	GGAGAGCAGGGAGGGAGG	60.446	72.222	0.00	0.00	0.00	4.30
476	507	2.445654	GAGAGCAGGGAGGGAGGG	60.446	72.222	0.00	0.00	0.00	4.30
525	573	8.723942	ACTTCCAGTGTTATCTCATTTCATAC	57.276	34.615	0.00	0.00	0.00	2.39
577	626	1.529010	CACCACACACTGGCCACAT	60.529	57.895	0.00	0.00	45.32	3.21
640	689	0.041833	TAGGCTGCTCTCCTCACCTT	59.958	55.000	0.00	0.00	35.21	3.50
768	817	0.179034	CTCTGCCCCTTGCTGATACC	60.179	60.000	0.00	0.00	45.47	2.73
769	818	1.524621	CTGCCCCTTGCTGATACCG	60.525	63.158	0.00	0.00	41.11	4.02
770	819	2.257409	CTGCCCCTTGCTGATACCGT	62.257	60.000	0.00	0.00	41.11	4.83
771	820	1.819632	GCCCCTTGCTGATACCGTG	60.820	63.158	0.00	0.00	36.87	4.94
772	821	1.904771	CCCCTTGCTGATACCGTGA	59.095	57.895	0.00	0.00	0.00	4.35
795	844	4.500116	GACGCTCGCTCTCCCCAC	62.500	72.222	0.00	0.00	0.00	4.61
822	871	4.632688	TCGCTACAACCTTTATTTACAGCC	59.367	41.667	0.00	0.00	0.00	4.85
825	874	5.646360	GCTACAACCTTTATTTACAGCCTCA	59.354	40.000	0.00	0.00	0.00	3.86
923	4532	4.430765	CCTGTCCGTCCCGTTCCG	62.431	72.222	0.00	0.00	0.00	4.30
1038	4654	3.428687	GATTCTGGGCTGAATCCCC	57.571	57.895	16.94	0.00	45.97	4.81
1065	4681	5.163612	GGATCTTGCTTTAGAATCCAACACC	60.164	44.000	0.00	0.00	0.00	4.16
1073	4689	6.127619	GCTTTAGAATCCAACACCTATTGCTT	60.128	38.462	0.00	0.00	0.00	3.91
1078	4694	8.000780	AGAATCCAACACCTATTGCTTTTATC	57.999	34.615	0.00	0.00	0.00	1.75
1091	4722	2.159324	GCTTTTATCTGCACTGCCTTCC	60.159	50.000	0.00	0.00	0.00	3.46
1104	4735	0.460284	GCCTTCCGATCTTTGCTCGA	60.460	55.000	0.00	0.00	38.38	4.04
1123	4754	1.834263	GACATCTGTACTCCCCTGCTT	59.166	52.381	0.00	0.00	0.00	3.91
1124	4755	1.834263	ACATCTGTACTCCCCTGCTTC	59.166	52.381	0.00	0.00	0.00	3.86
1132	4763	2.438075	CCCCTGCTTCAGCTCTGC	60.438	66.667	0.00	0.00	42.66	4.26
1284	4919	6.033513	GGTACGAGCAGCAATATTTTGTTTTC	59.966	38.462	0.00	0.00	35.17	2.29
1331	4981	0.463116	AAGCAAGGAACCGACGTTGT	60.463	50.000	1.30	0.00	37.76	3.32
1333	4983	1.155424	GCAAGGAACCGACGTTGTGA	61.155	55.000	1.30	0.00	37.76	3.58
1509	5177	1.136110	GAGAAGGAGGGCGAGAAGAAG	59.864	57.143	0.00	0.00	0.00	2.85
1583	5251	4.426313	GGACGGGGCCAAGAAGGG	62.426	72.222	4.39	0.00	38.09	3.95
1653	5321	3.254060	CGAGTTCATGAACCAGTACAGG	58.746	50.000	30.34	2.14	42.06	4.00
1659	5327	0.830444	TGAACCAGTACAGGTCGGCT	60.830	55.000	10.77	0.00	42.25	5.52
1735	5403	1.761174	GAGAACCCCAACTCCTGCA	59.239	57.895	0.00	0.00	0.00	4.41
1817	5485	0.389687	ACGCTGCTTGCTCTCTTCTC	60.390	55.000	0.00	0.00	40.11	2.87
1863	5531	1.152881	CAGTTATGGGCAGGGAGGC	60.153	63.158	0.00	0.00	43.27	4.70
1929	5597	1.606668	TGACCTGTGACGGCAATTTTC	59.393	47.619	0.00	0.00	0.00	2.29
1933	5601	3.886505	ACCTGTGACGGCAATTTTCTTTA	59.113	39.130	0.00	0.00	0.00	1.85
1945	5615	9.233232	CGGCAATTTTCTTTAAATATGTACTCC	57.767	33.333	0.00	0.00	35.39	3.85
1950	5620	7.852971	TTTCTTTAAATATGTACTCCCACCG	57.147	36.000	0.00	0.00	0.00	4.94
1952	5622	7.658525	TCTTTAAATATGTACTCCCACCGTA	57.341	36.000	0.00	0.00	0.00	4.02
1953	5623	8.076910	TCTTTAAATATGTACTCCCACCGTAA	57.923	34.615	0.00	0.00	0.00	3.18
1955	5625	8.721019	TTTAAATATGTACTCCCACCGTAAAG	57.279	34.615	0.00	0.00	0.00	1.85
1956	5626	6.549433	AAATATGTACTCCCACCGTAAAGA	57.451	37.500	0.00	0.00	0.00	2.52
1957	5627	6.549433	AATATGTACTCCCACCGTAAAGAA	57.451	37.500	0.00	0.00	0.00	2.52
1961	5631	6.549433	TGTACTCCCACCGTAAAGAAATAT	57.451	37.500	0.00	0.00	0.00	1.28
1966	5636	7.498443	ACTCCCACCGTAAAGAAATATAAGAG	58.502	38.462	0.00	0.00	0.00	2.85
1968	5638	5.176958	CCCACCGTAAAGAAATATAAGAGCG	59.823	44.000	0.00	0.00	0.00	5.03
1969	5639	5.751990	CCACCGTAAAGAAATATAAGAGCGT	59.248	40.000	0.00	0.00	0.00	5.07
1971	5641	7.201582	CCACCGTAAAGAAATATAAGAGCGTTT	60.202	37.037	0.00	0.00	0.00	3.60
1972	5642	8.810427	CACCGTAAAGAAATATAAGAGCGTTTA	58.190	33.333	0.00	0.00	0.00	2.01
1973	5643	9.028185	ACCGTAAAGAAATATAAGAGCGTTTAG	57.972	33.333	0.00	0.00	0.00	1.85
2000	5670	9.787532	AATACATATTATGAAAATATGCGCCAC	57.212	29.630	4.18	0.00	41.81	5.01
2007	5742	1.484038	AAATATGCGCCACCCATGTT	58.516	45.000	4.18	0.00	0.00	2.71
2065	5800	8.783093	CAAACTACAAAATGGATTAGTCTCACA	58.217	33.333	0.00	0.00	0.00	3.58
2091	5826	5.540337	TCTCTTTGCGAGGGATTAGTATCAT	59.460	40.000	0.00	0.00	40.30	2.45
2252	5991	6.569801	CGTCTTTTCAAAAAGGAGGAATACCC	60.570	42.308	13.68	0.00	44.22	3.69
2254	5993	4.750833	TTCAAAAAGGAGGAATACCCCA	57.249	40.909	0.00	0.00	36.73	4.96
2261	6000	1.512735	GAGGAATACCCCAGCCTCTT	58.487	55.000	0.00	0.00	42.81	2.85
2270	6009	0.034767	CCCAGCCTCTTCATCAAGCA	60.035	55.000	0.00	0.00	0.00	3.91
2271	6010	1.615116	CCCAGCCTCTTCATCAAGCAA	60.615	52.381	0.00	0.00	0.00	3.91
2272	6011	2.165167	CCAGCCTCTTCATCAAGCAAA	58.835	47.619	0.00	0.00	0.00	3.68
2333	6072	8.372459	AGGGAATTATATTAACATCTACGCACA	58.628	33.333	0.00	0.00	0.00	4.57
2413	6152	1.602377	CTCCGTCCCAAAACAAGTCAC	59.398	52.381	0.00	0.00	0.00	3.67
2414	6153	1.210967	TCCGTCCCAAAACAAGTCACT	59.789	47.619	0.00	0.00	0.00	3.41
2415	6154	1.333619	CCGTCCCAAAACAAGTCACTG	59.666	52.381	0.00	0.00	0.00	3.66
2416	6155	2.285083	CGTCCCAAAACAAGTCACTGA	58.715	47.619	0.00	0.00	0.00	3.41
2417	6156	2.878406	CGTCCCAAAACAAGTCACTGAT	59.122	45.455	0.00	0.00	0.00	2.90
2418	6157	3.315191	CGTCCCAAAACAAGTCACTGATT	59.685	43.478	0.00	0.00	0.00	2.57
2419	6158	4.202010	CGTCCCAAAACAAGTCACTGATTT	60.202	41.667	0.00	0.00	0.00	2.17
2420	6159	5.008217	CGTCCCAAAACAAGTCACTGATTTA	59.992	40.000	0.00	0.00	0.00	1.40
2421	6160	6.438763	GTCCCAAAACAAGTCACTGATTTAG	58.561	40.000	0.00	0.00	0.00	1.85
2422	6161	6.262273	GTCCCAAAACAAGTCACTGATTTAGA	59.738	38.462	0.00	0.00	0.00	2.10
2423	6162	6.831353	TCCCAAAACAAGTCACTGATTTAGAA	59.169	34.615	0.00	0.00	0.00	2.10
2424	6163	6.918022	CCCAAAACAAGTCACTGATTTAGAAC	59.082	38.462	0.00	0.00	0.00	3.01
2425	6164	7.201821	CCCAAAACAAGTCACTGATTTAGAACT	60.202	37.037	0.00	0.00	0.00	3.01
2426	6165	8.836413	CCAAAACAAGTCACTGATTTAGAACTA	58.164	33.333	0.00	0.00	0.00	2.24
2447	6186	9.612620	GAACTAAATCAGTGACACTTATTTTGG	57.387	33.333	25.20	20.60	34.78	3.28
2455	6194	4.273969	GTGACACTTATTTTGGAACGGACA	59.726	41.667	0.00	0.00	0.00	4.02
2534	6279	5.436175	AGTTTGTCTTGGGAAAATTTTGGG	58.564	37.500	8.47	0.00	0.00	4.12
2556	6301	4.941873	GGACTTCGAGTAATTTGGAATGGT	59.058	41.667	0.00	0.00	0.00	3.55
2682	6998	4.590850	AATGCCAACCAAGAAAGAGTTC	57.409	40.909	0.00	0.00	0.00	3.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
236	237	1.749634	CGATTTACTCGGAGTGGGAGT	59.250	52.381	20.58	3.65	46.05	3.85
250	251	0.391927	CCTGTGCGGGGTTCGATTTA	60.392	55.000	0.00	0.00	42.43	1.40
323	324	2.780010	CCCCACATCCTCTTGGTAGATT	59.220	50.000	0.00	0.00	34.23	2.40
376	381	3.956199	CAATTGGTATCAGAGGCCACAAT	59.044	43.478	5.01	0.00	31.19	2.71
419	424	0.748005	CCGTGCAATCGATCCCCTTT	60.748	55.000	0.00	0.00	0.00	3.11
432	440	1.568504	ACCTCTATTCTTCCCGTGCA	58.431	50.000	0.00	0.00	0.00	4.57
475	506	0.964358	TCTCGTTCCCCTTCGTCTCC	60.964	60.000	0.00	0.00	0.00	3.71
476	507	0.452585	CTCTCGTTCCCCTTCGTCTC	59.547	60.000	0.00	0.00	0.00	3.36
525	573	3.722147	CAGTCTGTAATTCTGGATCGGG	58.278	50.000	0.00	0.00	0.00	5.14
616	665	0.179086	GAGGAGAGCAGCCTAAGTGC	60.179	60.000	0.00	0.00	41.54	4.40
640	689	2.565391	AGTGTATCGGTGGACACATGAA	59.435	45.455	0.00	0.00	46.83	2.57
769	818	1.194896	GAGCGAGCGTCACGTATCAC	61.195	60.000	0.00	0.00	0.00	3.06
770	819	1.062047	GAGCGAGCGTCACGTATCA	59.938	57.895	0.00	0.00	0.00	2.15
771	820	0.655048	GAGAGCGAGCGTCACGTATC	60.655	60.000	0.00	0.00	0.00	2.24
772	821	1.352404	GAGAGCGAGCGTCACGTAT	59.648	57.895	0.00	0.00	0.00	3.06
795	844	2.304751	ATAAAGGTTGTAGCGACGGG	57.695	50.000	0.00	0.00	0.00	5.28
822	871	0.667993	GAGAGATGCCTCGAGGTGAG	59.332	60.000	31.43	7.71	44.08	3.51
825	874	1.040339	GTGGAGAGATGCCTCGAGGT	61.040	60.000	31.43	14.17	44.08	3.85
923	4532	4.509737	GGGAGGACGCGTACAGCC	62.510	72.222	25.94	23.27	44.76	4.85
933	4542	0.614979	TACAGACAGGCAGGGAGGAC	60.615	60.000	0.00	0.00	0.00	3.85
977	4593	2.027314	CGAGATGCGAGCTGAGGG	59.973	66.667	0.00	0.00	44.57	4.30
1038	4654	6.151648	TGTTGGATTCTAAAGCAAGATCCAAG	59.848	38.462	14.45	0.00	40.21	3.61
1065	4681	4.337555	AGGCAGTGCAGATAAAAGCAATAG	59.662	41.667	18.61	0.00	43.20	1.73
1073	4689	1.277842	TCGGAAGGCAGTGCAGATAAA	59.722	47.619	18.61	0.00	0.00	1.40
1078	4694	0.392193	AAGATCGGAAGGCAGTGCAG	60.392	55.000	18.61	2.52	0.00	4.41
1091	4722	2.534298	ACAGATGTCGAGCAAAGATCG	58.466	47.619	0.00	0.00	43.08	3.69
1104	4735	1.834263	GAAGCAGGGGAGTACAGATGT	59.166	52.381	0.00	0.00	0.00	3.06
1132	4763	0.725686	CAAGATGGCGTTCTGCTGAG	59.274	55.000	0.00	0.00	45.43	3.35
1246	4880	4.883300	GTACCGACGAGCGCCGAG	62.883	72.222	22.10	15.15	41.76	4.63
1272	4907	5.070770	TGCCATGCGAGAAAACAAAATAT	57.929	34.783	0.00	0.00	0.00	1.28
1284	4919	2.335752	CTAGCTCTTATGCCATGCGAG	58.664	52.381	0.00	0.00	0.00	5.03
1331	4981	0.673437	TGCACACACGAGACAGATCA	59.327	50.000	0.00	0.00	0.00	2.92
1333	4983	0.037882	CCTGCACACACGAGACAGAT	60.038	55.000	0.00	0.00	0.00	2.90
1659	5327	1.065272	GGGTTGTGGTAGGCCGAATAA	60.065	52.381	0.00	0.00	37.67	1.40
1668	5336	3.008594	TGTTCATGTAGGGGTTGTGGTAG	59.991	47.826	0.00	0.00	0.00	3.18
1735	5403	0.530744	TCGCGTTCTTAGCAGATGGT	59.469	50.000	5.77	0.00	34.19	3.55
1817	5485	1.058748	CAGAAACGGCATACACGCG	59.941	57.895	3.53	3.53	34.00	6.01
1863	5531	2.794350	GCAAAGTTTTCCACGTGAATGG	59.206	45.455	19.30	0.00	41.57	3.16
1929	5597	8.721019	TTTACGGTGGGAGTACATATTTAAAG	57.279	34.615	0.00	0.00	0.00	1.85
1933	5601	6.549433	TCTTTACGGTGGGAGTACATATTT	57.451	37.500	0.00	0.00	0.00	1.40
1945	5615	5.751990	ACGCTCTTATATTTCTTTACGGTGG	59.248	40.000	0.00	0.00	0.00	4.61
1976	5646	7.148154	GGGTGGCGCATATTTTCATAATATGTA	60.148	37.037	10.83	0.00	40.78	2.29
1977	5647	6.350110	GGGTGGCGCATATTTTCATAATATGT	60.350	38.462	10.83	0.00	40.78	2.29
1978	5648	6.035843	GGGTGGCGCATATTTTCATAATATG	58.964	40.000	10.83	11.36	41.31	1.78
2000	5670	3.689347	TCAGTGGATCTTCAAACATGGG	58.311	45.455	0.00	0.00	0.00	4.00
2007	5742	2.749076	CCGCAAATCAGTGGATCTTCAA	59.251	45.455	0.00	0.00	41.75	2.69
2091	5826	5.806502	CACCGTTGGAGTATAATCGTTAACA	59.193	40.000	6.39	0.00	0.00	2.41
2215	5952	9.129209	CTTTTTGAAAAGACGAAGAAAAGAACT	57.871	29.630	10.00	0.00	46.39	3.01
2216	5953	8.373256	CCTTTTTGAAAAGACGAAGAAAAGAAC	58.627	33.333	15.79	0.00	46.39	3.01
2219	5956	7.220875	CCTCCTTTTTGAAAAGACGAAGAAAAG	59.779	37.037	15.79	0.00	46.39	2.27
2228	5965	6.295123	GGGGTATTCCTCCTTTTTGAAAAGAC	60.295	42.308	15.79	5.84	40.60	3.01
2252	5991	1.830279	TTGCTTGATGAAGAGGCTGG	58.170	50.000	0.00	0.00	0.00	4.85
2384	6123	3.339713	TTTGGGACGGAGGGAGTATAT	57.660	47.619	0.00	0.00	0.00	0.86
2389	6128	0.109723	TTGTTTTGGGACGGAGGGAG	59.890	55.000	0.00	0.00	0.00	4.30
2421	6160	9.612620	CCAAAATAAGTGTCACTGATTTAGTTC	57.387	33.333	23.29	0.00	38.11	3.01
2422	6161	9.349713	TCCAAAATAAGTGTCACTGATTTAGTT	57.650	29.630	23.29	9.79	38.11	2.24
2423	6162	8.918202	TCCAAAATAAGTGTCACTGATTTAGT	57.082	30.769	23.29	10.38	38.11	2.24
2424	6163	9.612620	GTTCCAAAATAAGTGTCACTGATTTAG	57.387	33.333	23.29	18.43	38.11	1.85
2425	6164	8.286800	CGTTCCAAAATAAGTGTCACTGATTTA	58.713	33.333	23.29	9.79	38.11	1.40
2426	6165	7.138736	CGTTCCAAAATAAGTGTCACTGATTT	58.861	34.615	19.08	19.08	40.21	2.17
2427	6166	6.293955	CCGTTCCAAAATAAGTGTCACTGATT	60.294	38.462	9.52	9.52	30.51	2.57
2428	6167	5.181245	CCGTTCCAAAATAAGTGTCACTGAT	59.819	40.000	6.18	0.77	0.00	2.90
2429	6168	4.513692	CCGTTCCAAAATAAGTGTCACTGA	59.486	41.667	6.18	0.00	0.00	3.41
2430	6169	4.513692	TCCGTTCCAAAATAAGTGTCACTG	59.486	41.667	6.18	0.00	0.00	3.66
2431	6170	4.514066	GTCCGTTCCAAAATAAGTGTCACT	59.486	41.667	0.00	0.00	0.00	3.41
2432	6171	4.273969	TGTCCGTTCCAAAATAAGTGTCAC	59.726	41.667	0.00	0.00	0.00	3.67
2433	6172	4.452825	TGTCCGTTCCAAAATAAGTGTCA	58.547	39.130	0.00	0.00	0.00	3.58
2447	6186	7.277981	ACAACATCAAATATACTCTGTCCGTTC	59.722	37.037	0.00	0.00	0.00	3.95
2523	6268	8.699749	CAAATTACTCGAAGTCCCAAAATTTTC	58.300	33.333	0.00	0.00	25.87	2.29
2534	6279	5.163754	CCACCATTCCAAATTACTCGAAGTC	60.164	44.000	0.00	0.00	0.00	3.01
2556	6301	1.412453	AAACTACGCCACTGGTCCCA	61.412	55.000	0.00	0.00	0.00	4.37
2682	6998	4.458989	GTCATAGATGGAGAGGTCAGCTAG	59.541	50.000	0.00	0.00	36.70	3.42

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.