AutoCloner

Multiple sequence alignment - TraesCS6D01G203300

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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	TraesCS6D01G203300	chr6D	100.000	4761	0	0	1	4761	287031308	287026548	0.000000e+00	8793.0
1	TraesCS6D01G203300	chr6D	85.127	511	73	3	138	645	6830759	6831269	1.960000e-143	520.0
2	TraesCS6D01G203300	chr6B	93.998	4815	206	35	1	4761	447896539	447891754	0.000000e+00	7214.0
3	TraesCS6D01G203300	chr6B	84.449	508	70	8	138	639	646633723	646634227	4.280000e-135	492.0
4	TraesCS6D01G203300	chr6B	83.689	515	80	4	120	631	120822344	120822857	2.580000e-132	483.0
5	TraesCS6D01G203300	chr6A	94.679	2838	97	32	1884	4685	438577468	438580287	0.000000e+00	4355.0
6	TraesCS6D01G203300	chr6A	94.667	975	19	12	752	1704	438575917	438576880	0.000000e+00	1482.0
7	TraesCS6D01G203300	chr6A	88.805	661	59	6	1	659	438574863	438575510	0.000000e+00	797.0
8	TraesCS6D01G203300	chr6A	96.516	287	7	2	1601	1886	438576877	438577161	5.580000e-129	472.0
9	TraesCS6D01G203300	chr6A	90.323	124	10	2	1	124	172379633	172379512	1.370000e-35	161.0
10	TraesCS6D01G203300	chr6A	87.879	99	6	4	4588	4680	6418628	6418726	1.400000e-20	111.0
11	TraesCS6D01G203300	chr7D	82.630	616	79	18	123	734	104942005	104941414	1.960000e-143	520.0
12	TraesCS6D01G203300	chr7D	89.080	174	14	4	4588	4760	436466670	436466839	1.340000e-50	211.0
13	TraesCS6D01G203300	chr7D	88.506	174	15	4	4588	4760	292256294	292256463	6.250000e-49	206.0
14	TraesCS6D01G203300	chr7B	82.154	622	83	22	123	734	63626880	63626277	4.250000e-140	508.0
15	TraesCS6D01G203300	chr7B	89.256	121	13	0	1	121	592179111	592178991	8.250000e-33	152.0
16	TraesCS6D01G203300	chr1B	84.069	521	81	2	123	641	24793907	24794427	7.110000e-138	501.0
17	TraesCS6D01G203300	chr1D	83.333	522	79	7	120	638	470585405	470585921	4.310000e-130	475.0
18	TraesCS6D01G203300	chr1A	83.142	522	84	4	127	645	518085972	518086492	1.550000e-129	473.0
19	TraesCS6D01G203300	chr1A	89.474	57	2	2	1492	1544	5495572	5495516	8.550000e-08	69.4
20	TraesCS6D01G203300	chr1A	94.872	39	1	1	1491	1529	417383030	417382993	5.150000e-05	60.2
21	TraesCS6D01G203300	chr4A	88.506	174	16	4	4588	4760	107208661	107208831	1.740000e-49	207.0
22	TraesCS6D01G203300	chr4A	94.872	39	1	1	1491	1529	17251695	17251658	5.150000e-05	60.2
23	TraesCS6D01G203300	chr5D	93.388	121	8	0	1	121	350760253	350760373	3.790000e-41	180.0
24	TraesCS6D01G203300	chr5D	90.244	123	12	0	1	123	360752197	360752075	1.370000e-35	161.0
25	TraesCS6D01G203300	chr5B	81.407	199	37	0	2607	2805	526576295	526576493	3.810000e-36	163.0
26	TraesCS6D01G203300	chr2D	90.244	123	12	0	1	123	126757326	126757448	1.370000e-35	161.0
27	TraesCS6D01G203300	chr2D	85.965	57	2	3	1494	1544	84766348	84766292	6.660000e-04	56.5
28	TraesCS6D01G203300	chr4D	90.083	121	11	1	1	121	8134217	8134336	6.380000e-34	156.0
29	TraesCS6D01G203300	chr3B	89.167	120	12	1	1	119	100701095	100700976	1.070000e-31	148.0
30	TraesCS6D01G203300	chr7A	94.872	39	1	1	1491	1529	113801816	113801779	5.150000e-05	60.2
31	TraesCS6D01G203300	chr7A	94.872	39	1	1	1491	1529	672592602	672592639	5.150000e-05	60.2
32	TraesCS6D01G203300	chr2B	89.130	46	3	2	1480	1524	48872656	48872612	6.660000e-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	TraesCS6D01G203300	chr6D	287026548	287031308	4760	True	8793.0	8793	100.00000	1	4761	1	chr6D.!!$R1	4760
1	TraesCS6D01G203300	chr6D	6830759	6831269	510	False	520.0	520	85.12700	138	645	1	chr6D.!!$F1	507
2	TraesCS6D01G203300	chr6B	447891754	447896539	4785	True	7214.0	7214	93.99800	1	4761	1	chr6B.!!$R1	4760
3	TraesCS6D01G203300	chr6B	646633723	646634227	504	False	492.0	492	84.44900	138	639	1	chr6B.!!$F2	501
4	TraesCS6D01G203300	chr6B	120822344	120822857	513	False	483.0	483	83.68900	120	631	1	chr6B.!!$F1	511
5	TraesCS6D01G203300	chr6A	438574863	438580287	5424	False	1776.5	4355	93.66675	1	4685	4	chr6A.!!$F2	4684
6	TraesCS6D01G203300	chr7D	104941414	104942005	591	True	520.0	520	82.63000	123	734	1	chr7D.!!$R1	611
7	TraesCS6D01G203300	chr7B	63626277	63626880	603	True	508.0	508	82.15400	123	734	1	chr7B.!!$R1	611
8	TraesCS6D01G203300	chr1B	24793907	24794427	520	False	501.0	501	84.06900	123	641	1	chr1B.!!$F1	518
9	TraesCS6D01G203300	chr1D	470585405	470585921	516	False	475.0	475	83.33300	120	638	1	chr1D.!!$F1	518
10	TraesCS6D01G203300	chr1A	518085972	518086492	520	False	473.0	473	83.14200	127	645	1	chr1A.!!$F1	518

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
739	772	0.035739	GCGGTTAGGGTTCCTTGTCA	59.964	55.0	0.00	34.61	3.58	F
895	1326	0.463654	TGGCCTTTTCGATCCATCCG	60.464	55.0	3.32	0.00	4.18	F
898	1329	1.166531	CCTTTTCGATCCATCCGCCC	61.167	60.0	0.00	0.00	6.13	F
899	1330	0.463654	CTTTTCGATCCATCCGCCCA	60.464	55.0	0.00	0.00	5.36	F
2686	3573	1.882989	GCGGGCACAGAAGAGACTCT	61.883	60.0	0.00	0.00	3.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2686	3573	4.251268	CAATGCTGTGATGAGAACAGAGA	58.749	43.478	7.72	0.00	46.55	3.10	R
2819	3706	4.604843	TGTCAATTCTGCATCTAAAGCG	57.395	40.909	0.00	0.00	33.85	4.68	R
2984	3871	4.038642	TCCACCTTTATCTGTGTTTTTGCC	59.961	41.667	0.00	0.00	0.00	4.52	R
3065	3952	4.216257	ACACCCAGTGAATTCAGAATTTCG	59.784	41.667	8.80	0.00	36.96	3.46	R
4090	4979	0.247974	CGCTGCAGCAATAGAGTTGC	60.248	55.000	36.03	7.81	44.68	4.17	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
58	59	4.664677	GTCAGTGCCCGCAGACGT	62.665	66.667	0.00	0.00	37.70	4.34
99	100	2.721803	TTTGAGGGGGCGGATTTGCA	62.722	55.000	0.00	0.00	36.28	4.08
135	136	8.372459	TGTAGATGCTCTTACCAAAAGTAAAGA	58.628	33.333	0.00	0.00	40.43	2.52
202	204	1.256812	TCGAACTCAGATCTGGCACA	58.743	50.000	22.42	2.18	0.00	4.57
242	244	1.272147	GGAGGAGGAAACCATGCTTGT	60.272	52.381	0.00	0.00	0.00	3.16
298	300	3.867493	TCTTTCAGATGTCATCGATGCAC	59.133	43.478	20.81	18.13	0.00	4.57
335	337	1.972207	GCTCCTGGACTACCTCCCATT	60.972	57.143	0.00	0.00	38.49	3.16
377	379	2.549282	GTCGTTGCAATGACGCGT	59.451	55.556	30.35	13.85	40.16	6.01
416	424	3.055719	CAAAGATGCCGCCACCGT	61.056	61.111	0.00	0.00	0.00	4.83
459	467	3.019564	GACTGGTTCCCAAATCCATCAG	58.980	50.000	0.00	0.00	30.80	2.90
647	680	2.223805	CCTCATCACCGACGATCAATCA	60.224	50.000	0.00	0.00	0.00	2.57
648	681	2.791560	CTCATCACCGACGATCAATCAC	59.208	50.000	0.00	0.00	0.00	3.06
659	692	0.108329	ATCAATCACCACCGACGACC	60.108	55.000	0.00	0.00	0.00	4.79
660	693	1.005512	CAATCACCACCGACGACCA	60.006	57.895	0.00	0.00	0.00	4.02
661	694	0.601576	CAATCACCACCGACGACCAA	60.602	55.000	0.00	0.00	0.00	3.67
711	744	3.706373	GGTGGGCTCTCTTGGCGA	61.706	66.667	0.00	0.00	0.00	5.54
738	771	0.323957	AGCGGTTAGGGTTCCTTGTC	59.676	55.000	0.00	0.00	34.61	3.18
739	772	0.035739	GCGGTTAGGGTTCCTTGTCA	59.964	55.000	0.00	0.00	34.61	3.58
745	778	0.984995	AGGGTTCCTTGTCACTAGCC	59.015	55.000	0.00	0.00	0.00	3.93
805	1200	7.519008	GCAAAGAATCAAATACCCGATACAGAG	60.519	40.741	0.00	0.00	0.00	3.35
806	1201	6.732896	AGAATCAAATACCCGATACAGAGT	57.267	37.500	0.00	0.00	0.00	3.24
807	1202	7.125792	AGAATCAAATACCCGATACAGAGTT	57.874	36.000	0.00	0.00	0.00	3.01
808	1203	8.246430	AGAATCAAATACCCGATACAGAGTTA	57.754	34.615	0.00	0.00	0.00	2.24
809	1204	8.142551	AGAATCAAATACCCGATACAGAGTTAC	58.857	37.037	0.00	0.00	0.00	2.50
810	1205	6.778834	TCAAATACCCGATACAGAGTTACA	57.221	37.500	0.00	0.00	0.00	2.41
811	1206	6.802608	TCAAATACCCGATACAGAGTTACAG	58.197	40.000	0.00	0.00	0.00	2.74
812	1207	6.604396	TCAAATACCCGATACAGAGTTACAGA	59.396	38.462	0.00	0.00	0.00	3.41
835	1230	2.354199	GGACGAGCCTACACAGTAGTAC	59.646	54.545	0.00	0.00	0.00	2.73
894	1325	1.134098	TCTGGCCTTTTCGATCCATCC	60.134	52.381	3.32	0.00	0.00	3.51
895	1326	0.463654	TGGCCTTTTCGATCCATCCG	60.464	55.000	3.32	0.00	0.00	4.18
898	1329	1.166531	CCTTTTCGATCCATCCGCCC	61.167	60.000	0.00	0.00	0.00	6.13
899	1330	0.463654	CTTTTCGATCCATCCGCCCA	60.464	55.000	0.00	0.00	0.00	5.36
902	1333	4.626081	CGATCCATCCGCCCACCC	62.626	72.222	0.00	0.00	0.00	4.61
903	1334	4.626081	GATCCATCCGCCCACCCG	62.626	72.222	0.00	0.00	0.00	5.28
1247	1690	3.148279	GAGGGGTCGCATCCTCGT	61.148	66.667	0.00	0.00	39.95	4.18
1298	1741	4.617530	GCTTCCGTAAATTTTGGGTTCTCC	60.618	45.833	0.00	0.00	0.00	3.71
1330	1773	6.381481	TTTCGATGGATAAGCGTCTAGTTA	57.619	37.500	0.00	0.00	0.00	2.24
1412	1855	6.158598	GGGCCTTAAATTGTGTATATGCATG	58.841	40.000	10.16	0.00	0.00	4.06
1672	2219	8.947055	ACATCTGCTTTTCAGTTATTTTGTTT	57.053	26.923	0.00	0.00	43.32	2.83
1908	2765	9.515020	TTCAACTAATGTAAAAAGTGAAAGCAG	57.485	29.630	0.00	0.00	0.00	4.24
2172	3030	5.591067	AGTCCTCTATCGTTTCTTAGTCCAG	59.409	44.000	0.00	0.00	0.00	3.86
2175	3034	5.221087	CCTCTATCGTTTCTTAGTCCAGGTC	60.221	48.000	0.00	0.00	0.00	3.85
2177	3036	3.936372	TCGTTTCTTAGTCCAGGTCTG	57.064	47.619	0.00	0.00	0.00	3.51
2404	3289	6.561519	AGCACAAGGATATAAGGTACTGTT	57.438	37.500	0.00	0.00	40.86	3.16
2686	3573	1.882989	GCGGGCACAGAAGAGACTCT	61.883	60.000	0.00	0.00	0.00	3.24
2729	3616	7.276218	GCATTGCAATCATACAAAGAAGCTTTA	59.724	33.333	9.53	0.00	0.00	1.85
2819	3706	8.992835	AAAATTCTCTAATGAGCAAAATCACC	57.007	30.769	0.00	0.00	40.03	4.02
2984	3871	5.343249	CCTGTTCTTGACAACTTTGAAAGG	58.657	41.667	10.02	0.00	37.93	3.11
3065	3952	6.127897	ACCAGAGCATTTATAAGCAACTTGTC	60.128	38.462	0.18	0.00	0.00	3.18
3165	4052	7.823149	AGCAAGAAATGATATTTTGAACTGC	57.177	32.000	0.00	0.00	0.00	4.40
3664	4552	0.402121	GACCAGGCCCTGAAAAGTCT	59.598	55.000	13.74	0.00	32.44	3.24
3694	4582	7.024340	TGACGATACTACAATAGGTGAAGAC	57.976	40.000	0.00	0.00	0.00	3.01
3748	4636	3.614092	AGACGATGGTTTTGATGATGCT	58.386	40.909	0.00	0.00	0.00	3.79
3922	4810	9.299963	TGTTGATAATTGTGTCAAAAGTTTCTG	57.700	29.630	4.87	0.00	36.72	3.02
3930	4818	5.465390	TGTGTCAAAAGTTTCTGTATCCTCG	59.535	40.000	0.00	0.00	0.00	4.63
4023	4912	7.433719	CGAGGTAAATTGTGTTTGATTTGTTGA	59.566	33.333	0.00	0.00	0.00	3.18
4043	4932	5.514274	TGAAGATCCAAAAACCAGACAAC	57.486	39.130	0.00	0.00	0.00	3.32
4046	4935	6.486657	TGAAGATCCAAAAACCAGACAACTAG	59.513	38.462	0.00	0.00	0.00	2.57
4069	4958	2.497675	TCTGTGGCTTATCTCGCTTTCT	59.502	45.455	0.00	0.00	0.00	2.52
4070	4959	3.699538	TCTGTGGCTTATCTCGCTTTCTA	59.300	43.478	0.00	0.00	0.00	2.10
4078	4967	7.336931	TGGCTTATCTCGCTTTCTAATCTTTTT	59.663	33.333	0.00	0.00	0.00	1.94
4108	4997	3.618774	GCAACTCTATTGCTGCAGC	57.381	52.632	31.89	31.89	41.87	5.25
4109	4998	0.247974	GCAACTCTATTGCTGCAGCG	60.248	55.000	32.11	19.51	45.83	5.18
4110	4999	1.081892	CAACTCTATTGCTGCAGCGT	58.918	50.000	32.11	24.92	45.83	5.07
4112	5001	2.868583	CAACTCTATTGCTGCAGCGTAT	59.131	45.455	32.11	27.53	45.83	3.06
4113	5002	2.477825	ACTCTATTGCTGCAGCGTATG	58.522	47.619	32.11	21.65	45.83	2.39
4114	5003	2.101415	ACTCTATTGCTGCAGCGTATGA	59.899	45.455	32.11	24.21	45.83	2.15
4116	5005	3.320626	TCTATTGCTGCAGCGTATGATC	58.679	45.455	32.11	5.47	45.83	2.92
4117	5006	0.863799	ATTGCTGCAGCGTATGATCG	59.136	50.000	32.11	0.00	45.83	3.69
4118	5007	0.460109	TTGCTGCAGCGTATGATCGT	60.460	50.000	32.11	0.00	45.83	3.73
4119	5008	0.460109	TGCTGCAGCGTATGATCGTT	60.460	50.000	32.11	0.00	45.83	3.85
4120	5009	1.202359	TGCTGCAGCGTATGATCGTTA	60.202	47.619	32.11	8.56	45.83	3.18
4121	5010	1.190323	GCTGCAGCGTATGATCGTTAC	59.810	52.381	25.23	0.00	0.00	2.50
4261	5153	3.127030	GCCTTATCAAAAGTTCAGTCCCG	59.873	47.826	0.00	0.00	0.00	5.14
4336	5238	0.179174	AATCGAAACCGCGCAAATCC	60.179	50.000	8.75	0.00	0.00	3.01
4337	5239	1.024579	ATCGAAACCGCGCAAATCCT	61.025	50.000	8.75	0.00	0.00	3.24
4338	5240	0.390078	TCGAAACCGCGCAAATCCTA	60.390	50.000	8.75	0.00	0.00	2.94
4339	5241	0.026285	CGAAACCGCGCAAATCCTAG	59.974	55.000	8.75	0.00	0.00	3.02
4340	5242	0.377203	GAAACCGCGCAAATCCTAGG	59.623	55.000	8.75	0.82	0.00	3.02
4688	5590	5.231147	GTCTTTTGCTAGAAGCTACTCATCG	59.769	44.000	0.00	0.00	42.97	3.84
4752	5654	0.172578	TGCCGTCATAGAGTTCGTGG	59.827	55.000	0.00	0.00	0.00	4.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
92	93	0.598065	ACAGCCGGACTTTGCAAATC	59.402	50.000	13.23	11.89	0.00	2.17
99	100	0.905357	AGCATCTACAGCCGGACTTT	59.095	50.000	5.05	0.00	0.00	2.66
135	136	1.876799	TGATTCGTTCAACGGCAATGT	59.123	42.857	10.69	0.00	42.81	2.71
172	173	0.107703	TGAGTTCGATGGCATGTCCC	60.108	55.000	3.81	0.00	0.00	4.46
178	179	1.137675	CCAGATCTGAGTTCGATGGCA	59.862	52.381	24.62	0.00	0.00	4.92
202	204	1.288127	GCGTCTTAGTCGTGGTGGT	59.712	57.895	0.68	0.00	0.00	4.16
242	244	1.339631	GGGTTCGTGGTTGATGGATGA	60.340	52.381	0.00	0.00	0.00	2.92
298	300	2.812591	GGAGCAGATGCAGATTATGGTG	59.187	50.000	7.68	0.00	45.16	4.17
376	378	1.068741	GTGGACATGTATCCTCGGGAC	59.931	57.143	0.00	0.00	39.75	4.46
377	379	1.410004	GTGGACATGTATCCTCGGGA	58.590	55.000	0.00	0.00	39.75	5.14
416	424	2.046023	CAAGCAGGGATGCCGTGA	60.046	61.111	10.08	0.00	41.36	4.35
421	429	1.377202	TCCGTTCAAGCAGGGATGC	60.377	57.895	0.00	0.00	0.00	3.91
647	680	2.571216	CCTCTTGGTCGTCGGTGGT	61.571	63.158	0.00	0.00	0.00	4.16
648	681	2.261671	CCTCTTGGTCGTCGGTGG	59.738	66.667	0.00	0.00	0.00	4.61
659	692	3.997064	CTCCGCCAGCGACCTCTTG	62.997	68.421	14.67	0.00	42.83	3.02
660	693	3.764466	CTCCGCCAGCGACCTCTT	61.764	66.667	14.67	0.00	42.83	2.85
688	721	2.294078	AAGAGAGCCCACCCTTCCG	61.294	63.158	0.00	0.00	0.00	4.30
719	752	0.323957	GACAAGGAACCCTAACCGCT	59.676	55.000	0.00	0.00	31.13	5.52
724	757	2.570302	GGCTAGTGACAAGGAACCCTAA	59.430	50.000	0.00	0.00	31.13	2.69
805	1200	1.089920	TAGGCTCGTCCGTCTGTAAC	58.910	55.000	0.00	0.00	40.77	2.50
806	1201	1.089920	GTAGGCTCGTCCGTCTGTAA	58.910	55.000	0.00	0.00	40.77	2.41
807	1202	0.036105	TGTAGGCTCGTCCGTCTGTA	60.036	55.000	0.00	0.00	40.77	2.74
808	1203	1.303074	TGTAGGCTCGTCCGTCTGT	60.303	57.895	0.00	0.00	40.77	3.41
809	1204	1.136984	GTGTAGGCTCGTCCGTCTG	59.863	63.158	0.00	0.00	40.77	3.51
810	1205	1.303074	TGTGTAGGCTCGTCCGTCT	60.303	57.895	0.00	0.00	40.77	4.18
811	1206	1.136984	CTGTGTAGGCTCGTCCGTC	59.863	63.158	0.00	0.00	40.77	4.79
812	1207	0.321919	TACTGTGTAGGCTCGTCCGT	60.322	55.000	0.00	0.00	40.77	4.69
835	1230	1.464997	GGAAGCAGGTTCTTTGCGTAG	59.535	52.381	12.07	0.00	45.98	3.51
1298	1741	5.152097	GCTTATCCATCGAAAATCATGCAG	58.848	41.667	0.00	0.00	0.00	4.41
1330	1773	7.117285	TGTAACTCTGATAGCACATCTTCAT	57.883	36.000	0.00	0.00	0.00	2.57
1412	1855	0.039617	TATGCAAACTTGTGTGCGCC	60.040	50.000	4.18	0.00	43.93	6.53
1908	2765	7.941865	TGTGTACAAACGATAAATAGTTCGAC	58.058	34.615	0.00	0.00	38.67	4.20
2145	3003	6.974048	GGACTAAGAAACGATAGAGGACTTTC	59.026	42.308	0.00	0.00	41.38	2.62
2172	3030	6.295719	TGTTCTAAACCTAGAATCCAGACC	57.704	41.667	0.00	0.00	44.18	3.85
2404	3289	5.815233	TTTCCAACCTCAATATTGGCAAA	57.185	34.783	15.36	0.00	44.34	3.68
2532	3419	5.522460	TGTGCAAGGCTATTATTCTAACGAC	59.478	40.000	0.00	0.00	0.00	4.34
2686	3573	4.251268	CAATGCTGTGATGAGAACAGAGA	58.749	43.478	7.72	0.00	46.55	3.10
2729	3616	7.857569	CAACTTTTGCTTCATCATTGTTCATT	58.142	30.769	0.00	0.00	0.00	2.57
2765	3652	9.218525	TCATCCTCAATAGAAAGTAGAAAGGAT	57.781	33.333	0.00	0.00	40.78	3.24
2819	3706	4.604843	TGTCAATTCTGCATCTAAAGCG	57.395	40.909	0.00	0.00	33.85	4.68
2984	3871	4.038642	TCCACCTTTATCTGTGTTTTTGCC	59.961	41.667	0.00	0.00	0.00	4.52
3065	3952	4.216257	ACACCCAGTGAATTCAGAATTTCG	59.784	41.667	8.80	0.00	36.96	3.46
3664	4552	6.206829	CACCTATTGTAGTATCGTCATCTCCA	59.793	42.308	0.00	0.00	0.00	3.86
3694	4582	1.448540	CGCTTGAGGCCCTACACTG	60.449	63.158	0.00	0.00	37.74	3.66
3748	4636	0.546122	AGCCCAATTACTCGGCATCA	59.454	50.000	0.00	0.00	45.56	3.07
3922	4810	1.382522	TGACCGTACCACGAGGATAC	58.617	55.000	5.68	3.93	46.05	2.24
3930	4818	4.067972	ACCATGATAATGACCGTACCAC	57.932	45.455	0.00	0.00	0.00	4.16
4023	4912	6.601332	TCTAGTTGTCTGGTTTTTGGATCTT	58.399	36.000	0.00	0.00	0.00	2.40
4043	4932	3.505680	AGCGAGATAAGCCACAGATCTAG	59.494	47.826	0.00	0.00	34.64	2.43
4046	4935	2.810439	AGCGAGATAAGCCACAGATC	57.190	50.000	0.00	0.00	34.64	2.75
4069	4958	9.077885	AGTTGCTCTCCATTTACAAAAAGATTA	57.922	29.630	0.00	0.00	0.00	1.75
4070	4959	7.955918	AGTTGCTCTCCATTTACAAAAAGATT	58.044	30.769	0.00	0.00	0.00	2.40
4078	4967	5.586243	GCAATAGAGTTGCTCTCCATTTACA	59.414	40.000	1.54	0.00	43.71	2.41
4090	4979	0.247974	CGCTGCAGCAATAGAGTTGC	60.248	55.000	36.03	7.81	44.68	4.17
4103	4992	2.863401	AGTAACGATCATACGCTGCA	57.137	45.000	0.00	0.00	36.70	4.41
4107	4996	5.850128	ACGAGATAAAGTAACGATCATACGC	59.150	40.000	0.00	0.00	36.70	4.42
4120	5009	9.811995	TGCATTACAGTTTATACGAGATAAAGT	57.188	29.630	7.28	7.81	0.00	2.66
4138	5030	2.746904	CCATTTCACCGAGTGCATTACA	59.253	45.455	0.00	0.00	32.98	2.41
4140	5032	3.066291	ACCATTTCACCGAGTGCATTA	57.934	42.857	0.00	0.00	32.98	1.90
4261	5153	3.292159	GGACGGTTTGCCCCACAC	61.292	66.667	0.00	0.00	0.00	3.82
4688	5590	8.426881	TGCAATTTAGTAAGGGAAACAAAAAC	57.573	30.769	0.00	0.00	0.00	2.43

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.