AutoCloner

Multiple sequence alignment - TraesCS6A01G125600

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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	TraesCS6A01G125600	chr6A	100.000	5171	0	0	1	5171	99017169	99011999	0.000000e+00	9550.0
1	TraesCS6A01G125600	chr6A	88.637	4550	445	27	517	5017	98982838	98978312	0.000000e+00	5472.0
2	TraesCS6A01G125600	chr6A	86.294	4582	472	73	581	5047	98888523	98883983	0.000000e+00	4839.0
3	TraesCS6A01G125600	chr6A	80.248	3792	609	79	895	4595	98316058	98312316	0.000000e+00	2724.0
4	TraesCS6A01G125600	chr6A	80.391	2402	419	39	1841	4209	98916376	98913994	0.000000e+00	1779.0
5	TraesCS6A01G125600	chr6A	79.212	457	47	30	4648	5079	98913472	98913039	1.830000e-69	274.0
6	TraesCS6A01G125600	chr6A	80.665	331	27	15	189	486	98983261	98982935	6.740000e-54	222.0
7	TraesCS6A01G125600	chr6D	92.276	3431	255	5	868	4294	82220616	82217192	0.000000e+00	4859.0
8	TraesCS6A01G125600	chr6D	85.724	4280	486	70	851	5047	82204122	82199885	0.000000e+00	4403.0
9	TraesCS6A01G125600	chr6D	83.197	4273	611	63	116	4322	82238519	82234288	0.000000e+00	3814.0
10	TraesCS6A01G125600	chr6D	80.869	3544	581	63	895	4371	81926272	81922759	0.000000e+00	2699.0
11	TraesCS6A01G125600	chr6D	85.540	2455	315	23	571	2998	83108974	83106533	0.000000e+00	2531.0
12	TraesCS6A01G125600	chr6D	78.659	3908	693	90	526	4332	81935884	81932017	0.000000e+00	2466.0
13	TraesCS6A01G125600	chr6D	79.935	3409	585	66	982	4332	81773871	81770504	0.000000e+00	2414.0
14	TraesCS6A01G125600	chr6D	79.431	2567	436	60	1823	4320	82208964	82206421	0.000000e+00	1731.0
15	TraesCS6A01G125600	chr6D	82.055	730	70	19	4320	5017	82217192	82216492	2.700000e-157	566.0
16	TraesCS6A01G125600	chr6D	86.207	493	30	16	4675	5153	82233863	82233395	2.780000e-137	499.0
17	TraesCS6A01G125600	chr6D	91.292	356	19	7	518	873	82221870	82221527	4.690000e-130	475.0
18	TraesCS6A01G125600	chr6D	88.372	258	24	5	4702	4957	82205966	82205713	6.510000e-79	305.0
19	TraesCS6A01G125600	chr6D	99.115	113	1	0	1	113	82238934	82238822	2.440000e-48	204.0
20	TraesCS6A01G125600	chr6D	77.528	356	66	9	4664	5007	81922333	81921980	8.780000e-48	202.0
21	TraesCS6A01G125600	chr6D	89.091	165	12	4	326	486	82222130	82221968	3.160000e-47	200.0
22	TraesCS6A01G125600	chr6B	86.792	3763	407	45	647	4344	157109741	157106004	0.000000e+00	4113.0
23	TraesCS6A01G125600	chr6B	81.538	3862	617	49	517	4322	157489758	157485937	0.000000e+00	3094.0
24	TraesCS6A01G125600	chr6B	81.308	3365	565	43	895	4222	156654927	156651590	0.000000e+00	2671.0
25	TraesCS6A01G125600	chr6B	81.205	697	75	26	4436	5082	157485215	157484525	1.280000e-140	510.0
26	TraesCS6A01G125600	chr6B	79.882	676	83	35	4408	5047	157104006	157103348	3.670000e-121	446.0
27	TraesCS6A01G125600	chr6B	85.443	316	30	8	4653	4955	157127144	157126832	1.080000e-81	315.0
28	TraesCS6A01G125600	chr6B	89.552	134	9	3	359	489	157489983	157489852	1.150000e-36	165.0
29	TraesCS6A01G125600	chr6B	84.076	157	16	6	1	157	688656822	688656675	5.400000e-30	143.0
30	TraesCS6A01G125600	chr7D	73.579	2498	548	62	565	2995	560999793	561002245	0.000000e+00	854.0
31	TraesCS6A01G125600	chr7B	73.442	2278	530	45	777	2995	608900036	608902297	0.000000e+00	785.0
32	TraesCS6A01G125600	chr5D	81.250	96	16	2	721	816	372060546	372060453	5.550000e-10	76.8

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	TraesCS6A01G125600	chr6A	99011999	99017169	5170	True	9550.000000	9550	100.000000	1	5171	1	chr6A.!!$R3	5170
1	TraesCS6A01G125600	chr6A	98883983	98888523	4540	True	4839.000000	4839	86.294000	581	5047	1	chr6A.!!$R2	4466
2	TraesCS6A01G125600	chr6A	98978312	98983261	4949	True	2847.000000	5472	84.651000	189	5017	2	chr6A.!!$R5	4828
3	TraesCS6A01G125600	chr6A	98312316	98316058	3742	True	2724.000000	2724	80.248000	895	4595	1	chr6A.!!$R1	3700
4	TraesCS6A01G125600	chr6A	98913039	98916376	3337	True	1026.500000	1779	79.801500	1841	5079	2	chr6A.!!$R4	3238
5	TraesCS6A01G125600	chr6D	83106533	83108974	2441	True	2531.000000	2531	85.540000	571	2998	1	chr6D.!!$R3	2427
6	TraesCS6A01G125600	chr6D	81932017	81935884	3867	True	2466.000000	2466	78.659000	526	4332	1	chr6D.!!$R2	3806
7	TraesCS6A01G125600	chr6D	81770504	81773871	3367	True	2414.000000	2414	79.935000	982	4332	1	chr6D.!!$R1	3350
8	TraesCS6A01G125600	chr6D	82199885	82208964	9079	True	2146.333333	4403	84.509000	851	5047	3	chr6D.!!$R5	4196
9	TraesCS6A01G125600	chr6D	82216492	82222130	5638	True	1525.000000	4859	88.678500	326	5017	4	chr6D.!!$R6	4691
10	TraesCS6A01G125600	chr6D	82233395	82238934	5539	True	1505.666667	3814	89.506333	1	5153	3	chr6D.!!$R7	5152
11	TraesCS6A01G125600	chr6D	81921980	81926272	4292	True	1450.500000	2699	79.198500	895	5007	2	chr6D.!!$R4	4112
12	TraesCS6A01G125600	chr6B	156651590	156654927	3337	True	2671.000000	2671	81.308000	895	4222	1	chr6B.!!$R1	3327
13	TraesCS6A01G125600	chr6B	157103348	157109741	6393	True	2279.500000	4113	83.337000	647	5047	2	chr6B.!!$R4	4400
14	TraesCS6A01G125600	chr6B	157484525	157489983	5458	True	1256.333333	3094	84.098333	359	5082	3	chr6B.!!$R5	4723
15	TraesCS6A01G125600	chr7D	560999793	561002245	2452	False	854.000000	854	73.579000	565	2995	1	chr7D.!!$F1	2430
16	TraesCS6A01G125600	chr7B	608900036	608902297	2261	False	785.000000	785	73.442000	777	2995	1	chr7B.!!$F1	2218

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	Hairpin	End Stability	Orientation
724	1149	0.682852	TGGTACGGAAGGTGTTCAGG	59.317	55.000	33.93	3.86	F
1961	6912	0.174389	GAGCTGCCATCGACTCTGAA	59.826	55.000	0.00	3.02	F
2600	7551	1.002134	CTGCAACCCATTCGGACCT	60.002	57.895	34.64	3.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
2085	7036	1.337118	TGCTTTCCGGAATTTTGCCT	58.663	45.0	19.62	0.00	4.75	R
2857	7814	0.824595	TGCAGGCTGTTCAATGCAGT	60.825	50.0	17.16	43.34	4.40	R
4252	9478	1.651737	TGGCAACCTGTTAGGCTCTA	58.348	50.0	0.00	39.63	2.43	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
65	66	4.091509	CAGCGTGTTGAATTGGTAGTAGTC	59.908	45.833	0.00	0.00	0.00	2.59
255	556	5.243730	TCCAAATTCAGATGAAAACCAGTCC	59.756	40.000	0.00	0.00	37.61	3.85
276	577	3.494223	CCATATGGTCCACAATAGTGCGA	60.494	47.826	14.09	0.00	44.53	5.10
356	679	2.040278	CCTGGGTCAAGAGGATGAAACA	59.960	50.000	0.00	0.00	0.00	2.83
507	845	7.283354	GCAAGCACCTTCTAGAAATAATTACCT	59.717	37.037	6.63	0.00	0.00	3.08
508	846	8.831550	CAAGCACCTTCTAGAAATAATTACCTC	58.168	37.037	6.63	0.00	0.00	3.85
509	847	7.510407	AGCACCTTCTAGAAATAATTACCTCC	58.490	38.462	6.63	0.00	0.00	4.30
696	1103	7.979786	AGGAGGACTAGAAAATCTACAATGA	57.020	36.000	0.00	0.00	0.00	2.57
700	1107	9.308318	GAGGACTAGAAAATCTACAATGAAGTC	57.692	37.037	0.00	0.00	0.00	3.01
701	1108	8.261522	AGGACTAGAAAATCTACAATGAAGTCC	58.738	37.037	12.27	12.27	35.92	3.85
724	1149	0.682852	TGGTACGGAAGGTGTTCAGG	59.317	55.000	0.00	0.00	33.93	3.86
725	1150	0.971386	GGTACGGAAGGTGTTCAGGA	59.029	55.000	0.00	0.00	33.93	3.86
726	1151	1.345415	GGTACGGAAGGTGTTCAGGAA	59.655	52.381	0.00	0.00	33.93	3.36
729	1154	1.978580	ACGGAAGGTGTTCAGGAAGAT	59.021	47.619	0.00	0.00	33.93	2.40
738	1163	4.016444	GTGTTCAGGAAGATTGGGCAATA	58.984	43.478	0.00	0.00	0.00	1.90
807	1233	2.724977	TCAGTGTGAACTAGGAAGCG	57.275	50.000	0.00	0.00	0.00	4.68
845	1271	4.494484	GGCAGTTGTGTAAAATCCAATCC	58.506	43.478	0.00	0.00	0.00	3.01
910	5834	4.728772	TCTGCTTCTTTCTTTCCCATCAA	58.271	39.130	0.00	0.00	0.00	2.57
947	5873	5.121380	AGACCACCATTGATGCTTTATCT	57.879	39.130	0.00	0.00	36.71	1.98
970	5897	1.913419	TCAGGGGACAACATAACCTCC	59.087	52.381	0.00	0.00	0.00	4.30
977	5906	1.700739	ACAACATAACCTCCGGTTCCA	59.299	47.619	0.00	0.00	43.05	3.53
1020	5953	2.957402	TGCAGACACTCCATTTTCCT	57.043	45.000	0.00	0.00	0.00	3.36
1065	5998	1.843851	CACATACCTTCCCTTGGCCTA	59.156	52.381	3.32	0.00	0.00	3.93
1143	6079	2.424684	AGGACTCCCTTCTCCAGTTT	57.575	50.000	0.00	0.00	40.78	2.66
1175	6111	3.542676	ACAACACGGTGGCCTCGA	61.543	61.111	22.17	0.00	0.00	4.04
1252	6191	4.742440	GCACAGATGGGATTGTTACGGATA	60.742	45.833	0.00	0.00	0.00	2.59
1357	6296	3.272574	ACAATCTGCTATCTGGTGGTG	57.727	47.619	0.00	0.00	0.00	4.17
1593	6544	2.171003	GGGCAGCTACCAACTCATTTT	58.829	47.619	5.07	0.00	0.00	1.82
1865	6816	3.325293	TCTTGGAGAGAACAGCATCAC	57.675	47.619	0.00	0.00	0.00	3.06
1961	6912	0.174389	GAGCTGCCATCGACTCTGAA	59.826	55.000	0.00	0.00	0.00	3.02
2028	6979	2.142220	TGGAGAACTCGCCAAGGTT	58.858	52.632	0.00	0.00	42.86	3.50
2047	6998	5.188988	GGTTAATTTCTCCAACCTACCCT	57.811	43.478	0.60	0.00	38.93	4.34
2085	7036	4.955811	TCTTAGGAACAACAGCTTCAGA	57.044	40.909	0.00	0.00	0.00	3.27
2112	7063	2.981859	TTCCGGAAAGCATCTACTCC	57.018	50.000	16.28	0.00	0.00	3.85
2251	7202	6.615088	ACAAATATCACAAGTGCACTTCATC	58.385	36.000	28.97	0.00	33.11	2.92
2600	7551	1.002134	CTGCAACCCATTCGGACCT	60.002	57.895	0.00	0.00	34.64	3.85
2633	7584	9.606631	CTTTGAGTTACCAATTTATCTAGCTCT	57.393	33.333	0.00	0.00	0.00	4.09
2817	7774	1.279496	ATCTCACAAGCCTGCAGGTA	58.721	50.000	32.81	11.47	37.57	3.08
2857	7814	0.698238	CCTCACAGGTGGAATCCCAA	59.302	55.000	0.00	0.00	45.59	4.12
3056	8013	6.330278	TGATCCACTCAAAACTACGACATAG	58.670	40.000	0.00	0.00	36.89	2.23
3111	8068	3.254166	TCTTTGGAAGCATTGCTGTTCTC	59.746	43.478	12.82	5.72	39.62	2.87
3159	8116	5.175859	TCGATCAGAGTCAATGGTTTTACC	58.824	41.667	0.00	0.00	39.22	2.85
4252	9478	8.652810	ACTACGAGTTTGTTTGTACTTTGTAT	57.347	30.769	0.00	0.00	0.00	2.29
4416	11380	8.948853	ACAAAGTATAAACATGTGAAATGACG	57.051	30.769	0.00	0.00	29.77	4.35
4424	11388	5.287170	ACATGTGAAATGACGATCTTGTG	57.713	39.130	0.00	0.00	0.00	3.33
4452	11416	5.048782	TCGGTGAAAGATTGAAAATGGAGTG	60.049	40.000	0.00	0.00	0.00	3.51
4552	11580	4.994907	TTGCCGAATTACTAGCTACAGA	57.005	40.909	0.00	0.00	0.00	3.41
4597	11625	5.230182	GTGGAACAAATGGAATGAGAAACC	58.770	41.667	0.00	0.00	44.16	3.27
4598	11626	4.898265	TGGAACAAATGGAATGAGAAACCA	59.102	37.500	0.00	0.00	34.61	3.67
4599	11627	5.543405	TGGAACAAATGGAATGAGAAACCAT	59.457	36.000	0.00	0.00	44.87	3.55
4600	11628	6.101997	GGAACAAATGGAATGAGAAACCATC	58.898	40.000	0.00	0.00	42.59	3.51
4601	11629	6.071165	GGAACAAATGGAATGAGAAACCATCT	60.071	38.462	0.00	0.00	42.59	2.90
4615	11677	9.912634	TGAGAAACCATCTTTGAAATACAAATC	57.087	29.630	0.00	0.00	45.63	2.17
4618	11692	8.519492	AAACCATCTTTGAAATACAAATCACG	57.481	30.769	0.00	0.00	45.63	4.35
4651	11732	3.190744	CCACTAGCAGTCTAGAACACGAA	59.809	47.826	0.00	0.00	43.95	3.85
4660	11741	4.527038	AGTCTAGAACACGAAAGGAATGGA	59.473	41.667	0.00	0.00	0.00	3.41
4672	11779	4.792513	AAGGAATGGAGATCAGAAGCAT	57.207	40.909	0.00	0.00	0.00	3.79
4972	12139	2.087009	CGAACGTGGAAGCGAGGAC	61.087	63.158	0.00	0.00	35.59	3.85
5079	12260	4.394712	ACAGAGCGGGGAAAGCGG	62.395	66.667	0.00	0.00	40.04	5.52
5115	12296	2.258591	CTACAGCACTCCGCACGT	59.741	61.111	0.00	0.00	46.13	4.49
5116	12297	1.801913	CTACAGCACTCCGCACGTC	60.802	63.158	0.00	0.00	46.13	4.34
5130	12314	4.873129	CGTCCGCCGAGTGGGATG	62.873	72.222	0.00	0.00	39.56	3.51
5153	12337	2.227089	GATGGGCCGACTCACTCGTT	62.227	60.000	0.00	0.00	41.18	3.85
5154	12338	0.968901	ATGGGCCGACTCACTCGTTA	60.969	55.000	0.00	0.00	41.18	3.18
5155	12339	1.153881	GGGCCGACTCACTCGTTAC	60.154	63.158	0.00	0.00	41.18	2.50
5156	12340	1.593296	GGGCCGACTCACTCGTTACT	61.593	60.000	0.00	0.00	41.18	2.24
5157	12341	1.089920	GGCCGACTCACTCGTTACTA	58.910	55.000	0.00	0.00	41.18	1.82
5158	12342	1.063764	GGCCGACTCACTCGTTACTAG	59.936	57.143	0.00	0.00	41.18	2.57
5159	12343	1.063764	GCCGACTCACTCGTTACTAGG	59.936	57.143	0.00	0.00	41.18	3.02
5160	12344	2.354259	CCGACTCACTCGTTACTAGGT	58.646	52.381	0.00	0.00	41.18	3.08
5161	12345	2.746362	CCGACTCACTCGTTACTAGGTT	59.254	50.000	0.00	0.00	41.18	3.50
5162	12346	3.181512	CCGACTCACTCGTTACTAGGTTC	60.182	52.174	0.00	0.00	41.18	3.62
5163	12347	3.483248	CGACTCACTCGTTACTAGGTTCG	60.483	52.174	0.00	0.00	37.64	3.95
5164	12348	3.668447	ACTCACTCGTTACTAGGTTCGA	58.332	45.455	0.00	0.07	0.00	3.71
5165	12349	4.260170	ACTCACTCGTTACTAGGTTCGAT	58.740	43.478	0.00	0.00	0.00	3.59
5166	12350	4.332268	ACTCACTCGTTACTAGGTTCGATC	59.668	45.833	0.00	0.00	0.00	3.69
5167	12351	3.308053	TCACTCGTTACTAGGTTCGATCG	59.692	47.826	9.36	9.36	0.00	3.69
5168	12352	2.611292	ACTCGTTACTAGGTTCGATCGG	59.389	50.000	16.41	0.00	0.00	4.18
5169	12353	1.942657	TCGTTACTAGGTTCGATCGGG	59.057	52.381	16.41	1.87	0.00	5.14
5170	12354	1.672881	CGTTACTAGGTTCGATCGGGT	59.327	52.381	16.41	7.48	0.00	5.28

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
65	66	2.834549	AGTTGTGAGGGACATCTACAGG	59.165	50.000	0.00	0.00	33.56	4.00
118	419	9.113838	GGAACAAAGGGCTGATACATATATATG	57.886	37.037	19.21	19.21	39.55	1.78
127	428	0.733150	GCGGAACAAAGGGCTGATAC	59.267	55.000	0.00	0.00	0.00	2.24
157	458	4.252073	GTTCATCACTTGTCTCTGATGCT	58.748	43.478	3.25	0.00	42.40	3.79
158	459	3.061831	CGTTCATCACTTGTCTCTGATGC	59.938	47.826	3.25	0.00	42.40	3.91
180	481	2.033141	TCTGGCAGTGGCAAGCTC	59.967	61.111	20.97	4.49	41.16	4.09
255	556	3.727726	TCGCACTATTGTGGACCATATG	58.272	45.455	9.35	0.00	43.97	1.78
276	577	1.548582	CCATTGTCCTGGCTCCACTTT	60.549	52.381	0.00	0.00	0.00	2.66
356	679	3.690460	CCTGCTGGGTAATCTGTTCTTT	58.310	45.455	0.71	0.00	0.00	2.52
507	845	4.081309	CCTTTTGGGAACAGATAGTACGGA	60.081	45.833	0.00	0.00	44.54	4.69
508	846	4.189231	CCTTTTGGGAACAGATAGTACGG	58.811	47.826	0.00	0.00	44.54	4.02
509	847	3.621715	GCCTTTTGGGAACAGATAGTACG	59.378	47.826	0.00	0.00	44.54	3.67
542	940	7.009357	GCACTGAACTAAACTATTACTTCTCGG	59.991	40.741	0.00	0.00	0.00	4.63
696	1103	2.440627	ACCTTCCGTACCAAAAGGACTT	59.559	45.455	17.85	0.00	41.78	3.01
700	1107	2.265589	ACACCTTCCGTACCAAAAGG	57.734	50.000	11.95	11.95	44.23	3.11
701	1108	3.207778	TGAACACCTTCCGTACCAAAAG	58.792	45.455	0.00	0.00	0.00	2.27
706	1118	0.971386	TCCTGAACACCTTCCGTACC	59.029	55.000	0.00	0.00	0.00	3.34
724	1149	4.943705	TGACAAGTCTATTGCCCAATCTTC	59.056	41.667	1.53	0.00	32.50	2.87
725	1150	4.922206	TGACAAGTCTATTGCCCAATCTT	58.078	39.130	1.53	0.00	32.50	2.40
726	1151	4.018960	ACTGACAAGTCTATTGCCCAATCT	60.019	41.667	1.53	0.00	29.04	2.40
729	1154	3.788227	ACTGACAAGTCTATTGCCCAA	57.212	42.857	1.53	0.00	26.77	4.12
738	1163	5.984695	TGCTGTAATCTACTGACAAGTCT	57.015	39.130	1.53	0.00	37.88	3.24
845	1271	3.576982	TCCCTTGTAGTGGTAGTCAACAG	59.423	47.826	0.00	0.00	0.00	3.16
947	5873	3.773119	GAGGTTATGTTGTCCCCTGACTA	59.227	47.826	0.00	0.00	42.28	2.59
970	5897	1.798813	GTGAAACTAGCACTGGAACCG	59.201	52.381	0.00	0.00	33.57	4.44
977	5906	3.883489	GGTTTTCTGGTGAAACTAGCACT	59.117	43.478	0.00	0.00	46.13	4.40
1175	6111	2.827190	CATGCTGCCAGGACGCAT	60.827	61.111	9.47	9.47	44.53	4.73
1199	6135	1.975407	CCTTCCCACTGGCAGCAAG	60.975	63.158	15.89	11.23	0.00	4.01
1252	6191	2.433970	GACTCCTAGAAGCCAGCAAGAT	59.566	50.000	0.00	0.00	0.00	2.40
1383	6322	2.025155	ACGTCTACGATGAGGATGCTT	58.975	47.619	9.86	0.00	43.02	3.91
1431	6370	2.244695	TGGGTAGATGACAACTCGTGT	58.755	47.619	0.00	0.00	45.74	4.49
1666	6617	2.872408	GCATGGAGCAGCTACCAAA	58.128	52.632	15.11	0.00	44.79	3.28
1712	6663	3.304251	GGAGAGTCCCACTGAGGC	58.696	66.667	0.00	0.00	35.39	4.70
1764	6715	1.916777	GTTCCCGGGGAAGGAGACA	60.917	63.158	28.64	2.58	42.88	3.41
1961	6912	4.826733	TGGTTATGAGATTTGTGCAGTTGT	59.173	37.500	0.00	0.00	0.00	3.32
2028	6979	9.510062	TTTAGATAGGGTAGGTTGGAGAAATTA	57.490	33.333	0.00	0.00	0.00	1.40
2085	7036	1.337118	TGCTTTCCGGAATTTTGCCT	58.663	45.000	19.62	0.00	0.00	4.75
2134	7085	7.381323	CCATGGAAATTATTGAAAGATAGCCC	58.619	38.462	5.56	0.00	0.00	5.19
2251	7202	5.596361	TGAGATTCTTGGAGCTCCTAAGTAG	59.404	44.000	32.28	19.92	36.82	2.57
2633	7584	2.598589	GTACGCGGTATTGAAGTGACA	58.401	47.619	12.47	0.00	0.00	3.58
2704	7661	4.111577	TGACCAATCTCCAAGGGTATCTT	58.888	43.478	0.00	0.00	32.77	2.40
2791	7748	3.282021	GCAGGCTTGTGAGATTGGATAA	58.718	45.455	0.00	0.00	0.00	1.75
2817	7774	4.062991	GGTTGTTGGTCGACAAGTCTAAT	58.937	43.478	18.91	0.00	39.97	1.73
2857	7814	0.824595	TGCAGGCTGTTCAATGCAGT	60.825	50.000	17.16	0.00	43.34	4.40
2969	7926	2.035832	CCACACAACTTTGGATTCCCAC	59.964	50.000	0.00	0.00	43.41	4.61
3056	8013	1.347378	TGATTGCAAAAAGGGCCTTCC	59.653	47.619	21.20	9.08	0.00	3.46
3111	8068	2.281761	AGACGCCCCAGCAACAAG	60.282	61.111	0.00	0.00	39.83	3.16
3159	8116	6.040391	TGTTCTTCTCCCTTGTATTTTTGGTG	59.960	38.462	0.00	0.00	0.00	4.17
4252	9478	1.651737	TGGCAACCTGTTAGGCTCTA	58.348	50.000	0.00	0.00	39.63	2.43
4416	11380	6.910536	ATCTTTCACCGATAACACAAGATC	57.089	37.500	0.00	0.00	0.00	2.75
4424	11388	7.535139	TCCATTTTCAATCTTTCACCGATAAC	58.465	34.615	0.00	0.00	0.00	1.89
4452	11416	4.214971	CACATACTATCTGCCCTTGAATGC	59.785	45.833	0.00	0.00	0.00	3.56
4576	11604	5.467035	TGGTTTCTCATTCCATTTGTTCC	57.533	39.130	0.00	0.00	0.00	3.62
4600	11628	8.266693	CGTGCTGCGTGATTTGTATTTCAAAG	62.267	42.308	0.00	0.00	41.15	2.77
4601	11629	6.563674	CGTGCTGCGTGATTTGTATTTCAAA	61.564	40.000	0.00	0.00	41.60	2.69
4618	11692	3.494336	CTAGTGGCTGCGTGCTGC	61.494	66.667	14.42	14.42	46.70	5.25
4635	11709	3.299340	TCCTTTCGTGTTCTAGACTGC	57.701	47.619	0.00	0.00	0.00	4.40
4636	11710	4.627467	CCATTCCTTTCGTGTTCTAGACTG	59.373	45.833	0.00	0.00	0.00	3.51
4637	11711	4.527038	TCCATTCCTTTCGTGTTCTAGACT	59.473	41.667	0.00	0.00	0.00	3.24
4638	11712	4.817517	TCCATTCCTTTCGTGTTCTAGAC	58.182	43.478	0.00	0.00	0.00	2.59
4639	11713	4.770531	TCTCCATTCCTTTCGTGTTCTAGA	59.229	41.667	0.00	0.00	0.00	2.43
4641	11715	5.186992	TGATCTCCATTCCTTTCGTGTTCTA	59.813	40.000	0.00	0.00	0.00	2.10
4651	11732	4.792513	ATGCTTCTGATCTCCATTCCTT	57.207	40.909	0.00	0.00	0.00	3.36
4660	11741	5.339008	TGGTACGTAAATGCTTCTGATCT	57.661	39.130	0.00	0.00	0.00	2.75
4672	11779	4.829872	ATCCTTGGACATGGTACGTAAA	57.170	40.909	0.00	0.00	0.00	2.01
4783	11921	2.726822	GAACCCAGGTCGGCTCGTTT	62.727	60.000	0.00	0.00	0.00	3.60
4784	11922	3.236003	GAACCCAGGTCGGCTCGTT	62.236	63.158	0.00	0.00	0.00	3.85
4817	11968	1.305201	GTGTCTTTTCTTGGACCGCA	58.695	50.000	0.00	0.00	0.00	5.69
4899	12057	3.443045	CGCAATGCCGGCCTCTTT	61.443	61.111	26.77	9.68	0.00	2.52
5049	12227	3.144120	CTCTGTCGCCATCTCCCGG	62.144	68.421	0.00	0.00	0.00	5.73
5054	12232	3.842923	CCCGCTCTGTCGCCATCT	61.843	66.667	0.00	0.00	0.00	2.90
5063	12244	3.014085	TACCGCTTTCCCCGCTCTG	62.014	63.158	0.00	0.00	0.00	3.35
5084	12265	1.730772	GCTGTAGGCGATCGCTCTATG	60.731	57.143	36.25	27.05	41.60	2.23
5087	12268	2.121538	TGCTGTAGGCGATCGCTCT	61.122	57.895	36.25	30.76	45.43	4.09
5115	12296	3.770040	CACATCCCACTCGGCGGA	61.770	66.667	7.21	0.00	0.00	5.54
5116	12297	4.838152	CCACATCCCACTCGGCGG	62.838	72.222	7.21	0.00	0.00	6.13
5118	12299	2.746375	ATCCCACATCCCACTCGGC	61.746	63.158	0.00	0.00	0.00	5.54
5130	12314	3.399181	TGAGTCGGCCCATCCCAC	61.399	66.667	0.00	0.00	0.00	4.61

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.