AutoCloner

Multiple sequence alignment - TraesCS3D01G081200

Loading Multiple Alignment...

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	TraesCS3D01G081200	chr3D	100.000	3783	0	0	1	3783	40772894	40776676	0.000000e+00	6986
1	TraesCS3D01G081200	chr3D	98.284	874	15	0	2910	3783	448464897	448464024	0.000000e+00	1531
2	TraesCS3D01G081200	chr3D	93.220	177	9	3	1333	1509	40774151	40774324	1.350000e-64	257
3	TraesCS3D01G081200	chr3D	98.889	90	0	1	1	90	339967755	339967843	3.910000e-35	159
4	TraesCS3D01G081200	chr3D	93.878	98	5	1	1	98	395497525	395497429	3.050000e-31	147
5	TraesCS3D01G081200	chrUn	94.584	2585	98	25	79	2628	19785994	19783417	0.000000e+00	3960
6	TraesCS3D01G081200	chrUn	97.356	1437	20	2	1493	2911	19742818	19741382	0.000000e+00	2427
7	TraesCS3D01G081200	chrUn	96.440	1264	28	6	183	1431	19744437	19743176	0.000000e+00	2069
8	TraesCS3D01G081200	chrUn	93.277	595	14	4	2342	2911	19783667	19783074	0.000000e+00	854
9	TraesCS3D01G081200	chrUn	91.489	235	15	5	1333	1566	19784805	19784575	6.100000e-83	318
10	TraesCS3D01G081200	chrUn	93.782	193	9	3	1333	1525	19743349	19743160	1.720000e-73	287
11	TraesCS3D01G081200	chrUn	89.302	215	22	1	79	293	92963957	92963744	6.230000e-68	268
12	TraesCS3D01G081200	chr6A	92.922	1653	80	18	1271	2911	57424053	57425680	0.000000e+00	2370
13	TraesCS3D01G081200	chr6A	94.900	902	34	7	666	1563	57423374	57424267	0.000000e+00	1400
14	TraesCS3D01G081200	chr6A	94.350	177	7	3	1333	1509	57423962	57424135	6.230000e-68	268
15	TraesCS3D01G081200	chr6A	93.333	90	6	0	1271	1360	57424131	57424220	2.370000e-27	134
16	TraesCS3D01G081200	chr6B	89.020	1612	139	21	1320	2911	93017442	93019035	0.000000e+00	1962
17	TraesCS3D01G081200	chr6B	86.328	1280	96	23	676	1903	93101497	93102749	0.000000e+00	1321
18	TraesCS3D01G081200	chr6B	90.379	1029	65	11	1907	2911	93103526	93104544	0.000000e+00	1321
19	TraesCS3D01G081200	chr6B	85.846	325	17	11	676	984	93017132	93017443	6.100000e-83	318
20	TraesCS3D01G081200	chr6B	89.558	249	25	1	1307	1555	93102075	93102322	7.890000e-82	315
21	TraesCS3D01G081200	chr6B	92.500	80	6	0	1271	1350	93017471	93017550	8.590000e-22	115
22	TraesCS3D01G081200	chr6B	92.500	80	6	0	1271	1350	93102195	93102274	8.590000e-22	115
23	TraesCS3D01G081200	chr2D	98.398	874	13	1	2910	3783	627933279	627934151	0.000000e+00	1535
24	TraesCS3D01G081200	chr2D	85.949	548	39	12	79	598	615473927	615473390	5.520000e-153	551
25	TraesCS3D01G081200	chr2D	85.792	549	42	12	79	598	36236331	36236872	1.990000e-152	549
26	TraesCS3D01G081200	chr2D	85.793	542	42	15	79	593	558910265	558909732	3.320000e-150	542
27	TraesCS3D01G081200	chr2D	84.000	525	59	18	79	598	373764804	373765308	7.350000e-132	481
28	TraesCS3D01G081200	chr2D	94.949	99	4	1	1	99	68834855	68834952	1.820000e-33	154
29	TraesCS3D01G081200	chr2D	94.949	99	4	1	1	99	68892820	68892723	1.820000e-33	154
30	TraesCS3D01G081200	chr2D	93.137	102	4	3	1	101	441839795	441839696	3.050000e-31	147
31	TraesCS3D01G081200	chr1D	97.826	874	19	0	2910	3783	110003677	110002804	0.000000e+00	1509
32	TraesCS3D01G081200	chr1D	95.876	97	2	2	1	97	85486139	85486233	5.060000e-34	156
33	TraesCS3D01G081200	chr7D	97.254	874	24	0	2910	3783	183311079	183311952	0.000000e+00	1482
34	TraesCS3D01G081200	chr7D	84.954	545	43	17	79	598	631440058	631440588	2.010000e-142	516
35	TraesCS3D01G081200	chr5D	96.918	876	24	3	2910	3783	280763969	280764843	0.000000e+00	1465
36	TraesCS3D01G081200	chr5D	95.995	874	30	2	2910	3783	502865076	502864208	0.000000e+00	1415
37	TraesCS3D01G081200	chr5D	95.886	875	33	2	2910	3783	537374568	537373696	0.000000e+00	1413
38	TraesCS3D01G081200	chr5D	84.190	525	56	20	79	598	546675812	546676314	5.680000e-133	484
39	TraesCS3D01G081200	chr5D	83.704	540	36	20	79	593	396445216	396444704	2.660000e-126	462
40	TraesCS3D01G081200	chr4D	96.689	876	26	3	2910	3783	37501200	37502074	0.000000e+00	1454
41	TraesCS3D01G081200	chr4D	85.455	550	43	14	79	598	464169348	464169890	4.300000e-149	538
42	TraesCS3D01G081200	chr4D	83.206	524	62	18	79	598	296724810	296725311	1.240000e-124	457
43	TraesCS3D01G081200	chr4D	97.802	91	0	1	1	89	404904254	404904164	5.060000e-34	156
44	TraesCS3D01G081200	chr4D	95.745	94	0	4	1	94	381854823	381854912	8.470000e-32	148
45	TraesCS3D01G081200	chr6D	95.771	875	33	3	2910	3783	439677131	439676260	0.000000e+00	1408
46	TraesCS3D01G081200	chr6D	98.795	83	0	1	1	83	322994348	322994429	3.050000e-31	147
47	TraesCS3D01G081200	chr1A	91.776	535	25	5	79	598	482331266	482330736	0.000000e+00	726
48	TraesCS3D01G081200	chr5B	85.595	479	28	19	153	598	572740659	572740189	7.400000e-127	464
49	TraesCS3D01G081200	chr4B	85.132	491	32	19	153	608	650784589	650784105	7.400000e-127	464
50	TraesCS3D01G081200	chr4B	83.880	366	30	11	79	420	480830025	480829665	4.710000e-84	322

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	TraesCS3D01G081200	chr3D	40772894	40776676	3782	False	3621.500000	6986	96.610000	1	3783	2	chr3D.!!$F2	3782
1	TraesCS3D01G081200	chr3D	448464024	448464897	873	True	1531.000000	1531	98.284000	2910	3783	1	chr3D.!!$R2	873
2	TraesCS3D01G081200	chrUn	19783074	19785994	2920	True	1710.666667	3960	93.116667	79	2911	3	chrUn.!!$R3	2832
3	TraesCS3D01G081200	chrUn	19741382	19744437	3055	True	1594.333333	2427	95.859333	183	2911	3	chrUn.!!$R2	2728
4	TraesCS3D01G081200	chr6A	57423374	57425680	2306	False	1043.000000	2370	93.876250	666	2911	4	chr6A.!!$F1	2245
5	TraesCS3D01G081200	chr6B	93017132	93019035	1903	False	798.333333	1962	89.122000	676	2911	3	chr6B.!!$F1	2235
6	TraesCS3D01G081200	chr6B	93101497	93104544	3047	False	768.000000	1321	89.691250	676	2911	4	chr6B.!!$F2	2235
7	TraesCS3D01G081200	chr2D	627933279	627934151	872	False	1535.000000	1535	98.398000	2910	3783	1	chr2D.!!$F4	873
8	TraesCS3D01G081200	chr2D	615473390	615473927	537	True	551.000000	551	85.949000	79	598	1	chr2D.!!$R4	519
9	TraesCS3D01G081200	chr2D	36236331	36236872	541	False	549.000000	549	85.792000	79	598	1	chr2D.!!$F1	519
10	TraesCS3D01G081200	chr2D	558909732	558910265	533	True	542.000000	542	85.793000	79	593	1	chr2D.!!$R3	514
11	TraesCS3D01G081200	chr2D	373764804	373765308	504	False	481.000000	481	84.000000	79	598	1	chr2D.!!$F3	519
12	TraesCS3D01G081200	chr1D	110002804	110003677	873	True	1509.000000	1509	97.826000	2910	3783	1	chr1D.!!$R1	873
13	TraesCS3D01G081200	chr7D	183311079	183311952	873	False	1482.000000	1482	97.254000	2910	3783	1	chr7D.!!$F1	873
14	TraesCS3D01G081200	chr7D	631440058	631440588	530	False	516.000000	516	84.954000	79	598	1	chr7D.!!$F2	519
15	TraesCS3D01G081200	chr5D	280763969	280764843	874	False	1465.000000	1465	96.918000	2910	3783	1	chr5D.!!$F1	873
16	TraesCS3D01G081200	chr5D	502864208	502865076	868	True	1415.000000	1415	95.995000	2910	3783	1	chr5D.!!$R2	873
17	TraesCS3D01G081200	chr5D	537373696	537374568	872	True	1413.000000	1413	95.886000	2910	3783	1	chr5D.!!$R3	873
18	TraesCS3D01G081200	chr5D	546675812	546676314	502	False	484.000000	484	84.190000	79	598	1	chr5D.!!$F2	519
19	TraesCS3D01G081200	chr5D	396444704	396445216	512	True	462.000000	462	83.704000	79	593	1	chr5D.!!$R1	514
20	TraesCS3D01G081200	chr4D	37501200	37502074	874	False	1454.000000	1454	96.689000	2910	3783	1	chr4D.!!$F1	873
21	TraesCS3D01G081200	chr4D	464169348	464169890	542	False	538.000000	538	85.455000	79	598	1	chr4D.!!$F4	519
22	TraesCS3D01G081200	chr4D	296724810	296725311	501	False	457.000000	457	83.206000	79	598	1	chr4D.!!$F2	519
23	TraesCS3D01G081200	chr6D	439676260	439677131	871	True	1408.000000	1408	95.771000	2910	3783	1	chr6D.!!$R1	873
24	TraesCS3D01G081200	chr1A	482330736	482331266	530	True	726.000000	726	91.776000	79	598	1	chr1A.!!$R1	519

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
421	483	0.188342	AAAAGCCACACACCCCTCAT	59.812	50.0	0.0	0.0	0.0	2.90	F
1049	1143	0.617820	ACCACCCAGAGCTACCGATT	60.618	55.0	0.0	0.0	0.0	3.34	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1447	1640	0.100861	GGCGTAGAGTCAGTGTAGCC	59.899	60.0	0.0	0.0	36.32	3.93	R
2869	4266	0.608640	ACGGCTGACAGGGACTTAAG	59.391	55.0	0.0	0.0	34.60	1.85	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
22	23	3.073274	ACTCAAGGCAACCATTAGTCC	57.927	47.619	0.00	0.00	37.17	3.85
23	24	2.375174	ACTCAAGGCAACCATTAGTCCA	59.625	45.455	0.00	0.00	37.17	4.02
24	25	3.010584	ACTCAAGGCAACCATTAGTCCAT	59.989	43.478	0.00	0.00	37.17	3.41
25	26	4.227300	ACTCAAGGCAACCATTAGTCCATA	59.773	41.667	0.00	0.00	37.17	2.74
26	27	4.780815	TCAAGGCAACCATTAGTCCATAG	58.219	43.478	0.00	0.00	37.17	2.23
27	28	4.473196	TCAAGGCAACCATTAGTCCATAGA	59.527	41.667	0.00	0.00	37.17	1.98
28	29	4.696479	AGGCAACCATTAGTCCATAGAG	57.304	45.455	0.00	0.00	37.17	2.43
29	30	4.298626	AGGCAACCATTAGTCCATAGAGA	58.701	43.478	0.00	0.00	37.17	3.10
30	31	4.910304	AGGCAACCATTAGTCCATAGAGAT	59.090	41.667	0.00	0.00	37.17	2.75
31	32	5.370880	AGGCAACCATTAGTCCATAGAGATT	59.629	40.000	0.00	0.00	37.17	2.40
32	33	5.471456	GGCAACCATTAGTCCATAGAGATTG	59.529	44.000	0.00	0.00	0.00	2.67
33	34	6.058183	GCAACCATTAGTCCATAGAGATTGT	58.942	40.000	0.00	0.00	0.00	2.71
34	35	6.203723	GCAACCATTAGTCCATAGAGATTGTC	59.796	42.308	0.00	0.00	0.00	3.18
35	36	7.275183	CAACCATTAGTCCATAGAGATTGTCA	58.725	38.462	0.00	0.00	0.00	3.58
36	37	7.623999	ACCATTAGTCCATAGAGATTGTCAT	57.376	36.000	0.00	0.00	0.00	3.06
37	38	7.675062	ACCATTAGTCCATAGAGATTGTCATC	58.325	38.462	0.00	0.00	0.00	2.92
38	39	7.290948	ACCATTAGTCCATAGAGATTGTCATCA	59.709	37.037	0.00	0.00	0.00	3.07
39	40	8.152898	CCATTAGTCCATAGAGATTGTCATCAA	58.847	37.037	0.00	0.00	37.98	2.57
40	41	9.722184	CATTAGTCCATAGAGATTGTCATCAAT	57.278	33.333	0.00	0.00	45.57	2.57
44	45	8.153550	AGTCCATAGAGATTGTCATCAATTACC	58.846	37.037	0.00	0.00	43.33	2.85
45	46	7.933577	GTCCATAGAGATTGTCATCAATTACCA	59.066	37.037	0.00	0.00	43.33	3.25
46	47	8.493607	TCCATAGAGATTGTCATCAATTACCAA	58.506	33.333	0.00	0.00	43.33	3.67
47	48	9.123902	CCATAGAGATTGTCATCAATTACCAAA	57.876	33.333	0.00	0.00	43.33	3.28
50	51	7.830739	AGAGATTGTCATCAATTACCAAAACC	58.169	34.615	0.00	0.00	43.33	3.27
51	52	7.451255	AGAGATTGTCATCAATTACCAAAACCA	59.549	33.333	0.00	0.00	43.33	3.67
52	53	7.961351	AGATTGTCATCAATTACCAAAACCAA	58.039	30.769	0.00	0.00	43.33	3.67
53	54	8.428063	AGATTGTCATCAATTACCAAAACCAAA	58.572	29.630	0.00	0.00	43.33	3.28
54	55	7.778470	TTGTCATCAATTACCAAAACCAAAC	57.222	32.000	0.00	0.00	0.00	2.93
55	56	6.878317	TGTCATCAATTACCAAAACCAAACA	58.122	32.000	0.00	0.00	0.00	2.83
56	57	7.504403	TGTCATCAATTACCAAAACCAAACAT	58.496	30.769	0.00	0.00	0.00	2.71
57	58	7.440556	TGTCATCAATTACCAAAACCAAACATG	59.559	33.333	0.00	0.00	0.00	3.21
58	59	6.933521	TCATCAATTACCAAAACCAAACATGG	59.066	34.615	0.00	0.00	38.91	3.66
59	60	5.615289	TCAATTACCAAAACCAAACATGGG	58.385	37.500	0.00	0.00	37.26	4.00
60	61	4.632327	ATTACCAAAACCAAACATGGGG	57.368	40.909	0.00	0.00	37.26	4.96
61	62	1.135960	ACCAAAACCAAACATGGGGG	58.864	50.000	0.00	0.00	37.26	5.40
62	63	0.250684	CCAAAACCAAACATGGGGGC	60.251	55.000	0.00	0.00	0.00	5.80
63	64	0.471617	CAAAACCAAACATGGGGGCA	59.528	50.000	0.00	0.00	0.00	5.36
64	65	0.472044	AAAACCAAACATGGGGGCAC	59.528	50.000	0.00	0.00	0.00	5.01
76	77	3.365535	GGGCACCGCATGTTCTTT	58.634	55.556	0.00	0.00	40.86	2.52
77	78	1.212751	GGGCACCGCATGTTCTTTC	59.787	57.895	0.00	0.00	40.86	2.62
337	393	2.300437	AGCCCTATTAATCGCTCCTGTC	59.700	50.000	0.00	0.00	0.00	3.51
350	409	2.203139	CTGTCCCCACGCAACACA	60.203	61.111	0.00	0.00	0.00	3.72
421	483	0.188342	AAAAGCCACACACCCCTCAT	59.812	50.000	0.00	0.00	0.00	2.90
594	662	2.921754	CGAAGGTCAAAGTACATCGACC	59.078	50.000	15.95	15.95	46.85	4.79
603	671	5.643348	TCAAAGTACATCGACCGAGTTACTA	59.357	40.000	12.95	0.81	30.28	1.82
628	696	2.358939	AAGTACATTCGTGTCCGTCC	57.641	50.000	0.00	0.00	35.01	4.79
646	715	3.368116	CGTCCCCTTAAAACTCACTCGAT	60.368	47.826	0.00	0.00	0.00	3.59
1049	1143	0.617820	ACCACCCAGAGCTACCGATT	60.618	55.000	0.00	0.00	0.00	3.34
1458	1651	2.184579	GCGGGAGGCTACACTGAC	59.815	66.667	0.00	0.00	39.11	3.51
1459	1652	2.352032	GCGGGAGGCTACACTGACT	61.352	63.158	0.00	0.00	39.11	3.41
1460	1653	1.810532	CGGGAGGCTACACTGACTC	59.189	63.158	0.00	0.00	41.23	3.36
1461	1654	0.681564	CGGGAGGCTACACTGACTCT	60.682	60.000	0.00	0.00	41.65	3.24
1468	1667	0.377554	CTACACTGACTCTACGCCGG	59.622	60.000	0.00	0.00	0.00	6.13
2193	3497	4.722008	GCGTTCAAAAAGGCCGTT	57.278	50.000	0.00	0.00	39.74	4.44
2575	3969	1.476845	TACCAAGTCCGCTGCCAAGA	61.477	55.000	0.00	0.00	0.00	3.02
2869	4266	2.555757	GCAATCCCCATGATAAGTCAGC	59.444	50.000	0.00	0.00	37.87	4.26
2907	4304	6.479990	CAGCCGTGATAAATCTTCAGTTATGA	59.520	38.462	0.00	0.00	0.00	2.15
3016	4414	7.168905	CCTAACAAATAGAGGAGTGAAACCTT	58.831	38.462	0.00	0.00	37.93	3.50
3032	4430	1.766496	ACCTTCAACCGAGAAGAACCA	59.234	47.619	12.00	0.00	46.18	3.67
3352	4751	2.875672	GCACATGGTCCACTTGAGCTAA	60.876	50.000	7.43	0.00	42.12	3.09
3509	4908	0.314935	CACAATGGACGGCAAGCTTT	59.685	50.000	0.00	0.00	0.00	3.51
3699	5098	5.334879	GGTTAGTACACAAAGCACAATGGAG	60.335	44.000	0.00	0.00	0.00	3.86
3769	5168	5.053811	TCTACGCTTTGTGAGTTGATCAAA	58.946	37.500	10.35	0.00	40.43	2.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	4.042311	TGGACTAATGGTTGCCTTGAGTTA	59.958	41.667	0.00	0.00	0.00	2.24
1	2	3.181434	TGGACTAATGGTTGCCTTGAGTT	60.181	43.478	0.00	0.00	0.00	3.01
2	3	2.375174	TGGACTAATGGTTGCCTTGAGT	59.625	45.455	0.00	0.00	0.00	3.41
3	4	3.071874	TGGACTAATGGTTGCCTTGAG	57.928	47.619	0.00	0.00	0.00	3.02
4	5	3.737559	ATGGACTAATGGTTGCCTTGA	57.262	42.857	0.00	0.00	0.00	3.02
5	6	4.780815	TCTATGGACTAATGGTTGCCTTG	58.219	43.478	0.00	0.00	0.00	3.61
6	7	4.721776	TCTCTATGGACTAATGGTTGCCTT	59.278	41.667	0.00	0.00	0.00	4.35
7	8	4.298626	TCTCTATGGACTAATGGTTGCCT	58.701	43.478	0.00	0.00	0.00	4.75
8	9	4.689612	TCTCTATGGACTAATGGTTGCC	57.310	45.455	0.00	0.00	0.00	4.52
9	10	6.058183	ACAATCTCTATGGACTAATGGTTGC	58.942	40.000	0.00	0.00	0.00	4.17
10	11	7.275183	TGACAATCTCTATGGACTAATGGTTG	58.725	38.462	0.00	0.00	0.00	3.77
11	12	7.437713	TGACAATCTCTATGGACTAATGGTT	57.562	36.000	0.00	0.00	0.00	3.67
12	13	7.290948	TGATGACAATCTCTATGGACTAATGGT	59.709	37.037	0.00	0.00	33.61	3.55
13	14	7.674120	TGATGACAATCTCTATGGACTAATGG	58.326	38.462	0.00	0.00	33.61	3.16
14	15	9.722184	ATTGATGACAATCTCTATGGACTAATG	57.278	33.333	0.00	0.00	42.20	1.90
18	19	8.153550	GGTAATTGATGACAATCTCTATGGACT	58.846	37.037	0.00	0.00	44.67	3.85
19	20	7.933577	TGGTAATTGATGACAATCTCTATGGAC	59.066	37.037	0.00	0.00	44.67	4.02
20	21	8.033178	TGGTAATTGATGACAATCTCTATGGA	57.967	34.615	0.00	0.00	44.67	3.41
21	22	8.681486	TTGGTAATTGATGACAATCTCTATGG	57.319	34.615	0.00	0.00	44.67	2.74
24	25	8.956426	GGTTTTGGTAATTGATGACAATCTCTA	58.044	33.333	0.00	0.00	44.67	2.43
25	26	7.451255	TGGTTTTGGTAATTGATGACAATCTCT	59.549	33.333	0.00	0.00	44.67	3.10
26	27	7.601856	TGGTTTTGGTAATTGATGACAATCTC	58.398	34.615	0.00	0.00	44.67	2.75
27	28	7.537596	TGGTTTTGGTAATTGATGACAATCT	57.462	32.000	0.00	0.00	44.67	2.40
28	29	8.495148	GTTTGGTTTTGGTAATTGATGACAATC	58.505	33.333	0.00	0.00	44.67	2.67
29	30	7.989741	TGTTTGGTTTTGGTAATTGATGACAAT	59.010	29.630	0.00	0.00	46.99	2.71
30	31	7.331026	TGTTTGGTTTTGGTAATTGATGACAA	58.669	30.769	0.00	0.00	40.42	3.18
31	32	6.878317	TGTTTGGTTTTGGTAATTGATGACA	58.122	32.000	0.00	0.00	0.00	3.58
32	33	7.095271	CCATGTTTGGTTTTGGTAATTGATGAC	60.095	37.037	0.00	0.00	38.30	3.06
33	34	6.933521	CCATGTTTGGTTTTGGTAATTGATGA	59.066	34.615	0.00	0.00	38.30	2.92
34	35	6.149142	CCCATGTTTGGTTTTGGTAATTGATG	59.851	38.462	0.00	0.00	41.91	3.07
35	36	6.237154	CCCATGTTTGGTTTTGGTAATTGAT	58.763	36.000	0.00	0.00	41.91	2.57
36	37	5.455326	CCCCATGTTTGGTTTTGGTAATTGA	60.455	40.000	0.00	0.00	41.91	2.57
37	38	4.759183	CCCCATGTTTGGTTTTGGTAATTG	59.241	41.667	0.00	0.00	41.91	2.32
38	39	4.202514	CCCCCATGTTTGGTTTTGGTAATT	60.203	41.667	0.00	0.00	41.91	1.40
39	40	3.329225	CCCCCATGTTTGGTTTTGGTAAT	59.671	43.478	0.00	0.00	41.91	1.89
40	41	2.706190	CCCCCATGTTTGGTTTTGGTAA	59.294	45.455	0.00	0.00	41.91	2.85
41	42	2.330216	CCCCCATGTTTGGTTTTGGTA	58.670	47.619	0.00	0.00	41.91	3.25
42	43	1.135960	CCCCCATGTTTGGTTTTGGT	58.864	50.000	0.00	0.00	41.91	3.67
43	44	0.250684	GCCCCCATGTTTGGTTTTGG	60.251	55.000	0.00	0.00	41.91	3.28
44	45	0.471617	TGCCCCCATGTTTGGTTTTG	59.528	50.000	0.00	0.00	41.91	2.44
45	46	0.472044	GTGCCCCCATGTTTGGTTTT	59.528	50.000	0.00	0.00	41.91	2.43
46	47	1.414866	GGTGCCCCCATGTTTGGTTT	61.415	55.000	0.00	0.00	41.91	3.27
47	48	1.841103	GGTGCCCCCATGTTTGGTT	60.841	57.895	0.00	0.00	41.91	3.67
48	49	2.203773	GGTGCCCCCATGTTTGGT	60.204	61.111	0.00	0.00	41.91	3.67
49	50	3.381136	CGGTGCCCCCATGTTTGG	61.381	66.667	0.00	0.00	43.23	3.28
50	51	4.067913	GCGGTGCCCCCATGTTTG	62.068	66.667	0.00	0.00	0.00	2.93
51	52	3.903281	ATGCGGTGCCCCCATGTTT	62.903	57.895	0.00	0.00	0.00	2.83
52	53	4.380945	ATGCGGTGCCCCCATGTT	62.381	61.111	0.00	0.00	0.00	2.71
55	56	4.380945	AACATGCGGTGCCCCCAT	62.381	61.111	0.00	0.00	0.00	4.00
57	58	4.740822	AGAACATGCGGTGCCCCC	62.741	66.667	0.00	0.00	0.00	5.40
58	59	2.212900	GAAAGAACATGCGGTGCCCC	62.213	60.000	0.00	0.00	0.00	5.80
59	60	1.212751	GAAAGAACATGCGGTGCCC	59.787	57.895	0.00	0.00	0.00	5.36
60	61	0.387239	GTGAAAGAACATGCGGTGCC	60.387	55.000	0.00	0.00	0.00	5.01
61	62	0.310543	TGTGAAAGAACATGCGGTGC	59.689	50.000	0.00	0.00	0.00	5.01
62	63	2.995466	ATGTGAAAGAACATGCGGTG	57.005	45.000	0.00	0.00	39.32	4.94
63	64	3.407698	TGTATGTGAAAGAACATGCGGT	58.592	40.909	0.00	0.00	43.64	5.68
64	65	4.621068	ATGTATGTGAAAGAACATGCGG	57.379	40.909	0.00	0.00	43.64	5.69
65	66	6.105657	TGTATGTATGTGAAAGAACATGCG	57.894	37.500	0.00	0.00	43.64	4.73
66	67	7.530010	AGTTGTATGTATGTGAAAGAACATGC	58.470	34.615	0.00	0.00	40.93	4.06
77	78	6.090763	CGGCCACATATAGTTGTATGTATGTG	59.909	42.308	2.24	14.29	46.53	3.21
296	321	1.902508	TGTTGGCTTTGGTTTGTTCCA	59.097	42.857	0.00	0.00	35.49	3.53
312	367	2.808543	GGAGCGATTAATAGGGCTGTTG	59.191	50.000	11.56	0.00	35.54	3.33
337	393	3.215568	TGCTTGTGTTGCGTGGGG	61.216	61.111	0.00	0.00	0.00	4.96
350	409	4.829492	AGGCTGAATTTTCTGTTAGTGCTT	59.171	37.500	0.00	0.00	0.00	3.91
544	611	5.405935	TTCTGTTTGAGATTCAGGATCGA	57.594	39.130	0.00	0.00	39.85	3.59
611	679	0.459063	GGGGACGGACACGAATGTAC	60.459	60.000	0.00	0.00	44.60	2.90
612	680	0.612732	AGGGGACGGACACGAATGTA	60.613	55.000	0.00	0.00	44.60	2.29
613	681	1.477685	AAGGGGACGGACACGAATGT	61.478	55.000	0.00	0.00	44.60	2.71
614	682	0.533491	TAAGGGGACGGACACGAATG	59.467	55.000	0.00	0.00	44.60	2.67
615	683	1.269012	TTAAGGGGACGGACACGAAT	58.731	50.000	0.00	0.00	44.60	3.34
616	684	1.047002	TTTAAGGGGACGGACACGAA	58.953	50.000	0.00	0.00	44.60	3.85
620	688	2.048601	TGAGTTTTAAGGGGACGGACA	58.951	47.619	0.00	0.00	0.00	4.02
621	689	2.038164	AGTGAGTTTTAAGGGGACGGAC	59.962	50.000	0.00	0.00	0.00	4.79
623	691	2.696506	GAGTGAGTTTTAAGGGGACGG	58.303	52.381	0.00	0.00	0.00	4.79
624	692	2.029649	TCGAGTGAGTTTTAAGGGGACG	60.030	50.000	0.00	0.00	0.00	4.79
626	694	4.285003	TCAATCGAGTGAGTTTTAAGGGGA	59.715	41.667	12.21	0.00	0.00	4.81
628	696	5.786401	CTCAATCGAGTGAGTTTTAAGGG	57.214	43.478	29.64	6.64	40.22	3.95
646	715	1.061546	AGGGGACGGCTAAAACTCAA	58.938	50.000	0.00	0.00	0.00	3.02
1049	1143	1.018840	TGGAGGGAGGAAGAGGATCA	58.981	55.000	0.00	0.00	37.82	2.92
1432	1625	1.400530	TAGCCTCCCGCCTTCTTAGC	61.401	60.000	0.00	0.00	38.78	3.09
1434	1627	0.324923	TGTAGCCTCCCGCCTTCTTA	60.325	55.000	0.00	0.00	38.78	2.10
1438	1631	2.284699	AGTGTAGCCTCCCGCCTT	60.285	61.111	0.00	0.00	38.78	4.35
1439	1632	3.077556	CAGTGTAGCCTCCCGCCT	61.078	66.667	0.00	0.00	38.78	5.52
1440	1633	3.075005	TCAGTGTAGCCTCCCGCC	61.075	66.667	0.00	0.00	38.78	6.13
1443	1636	2.025898	GTAGAGTCAGTGTAGCCTCCC	58.974	57.143	0.00	0.00	0.00	4.30
1445	1638	1.064357	GCGTAGAGTCAGTGTAGCCTC	59.936	57.143	0.00	0.00	0.00	4.70
1446	1639	1.096416	GCGTAGAGTCAGTGTAGCCT	58.904	55.000	0.00	0.00	0.00	4.58
1447	1640	0.100861	GGCGTAGAGTCAGTGTAGCC	59.899	60.000	0.00	0.00	36.32	3.93
1450	1643	1.651240	GCCGGCGTAGAGTCAGTGTA	61.651	60.000	12.58	0.00	0.00	2.90
1451	1644	2.991076	GCCGGCGTAGAGTCAGTGT	61.991	63.158	12.58	0.00	0.00	3.55
1452	1645	2.202623	GCCGGCGTAGAGTCAGTG	60.203	66.667	12.58	0.00	0.00	3.66
1453	1646	3.450115	GGCCGGCGTAGAGTCAGT	61.450	66.667	22.54	0.00	0.00	3.41
1458	1651	4.253257	GAGTCGGCCGGCGTAGAG	62.253	72.222	26.29	9.24	0.00	2.43
2193	3497	4.467084	GAGGTGGCGGCGGATTCA	62.467	66.667	9.78	0.00	0.00	2.57
2869	4266	0.608640	ACGGCTGACAGGGACTTAAG	59.391	55.000	0.00	0.00	34.60	1.85
2907	4304	6.015940	CCTCTTTCCAACAAGCTTGAGTTTAT	60.016	38.462	32.50	6.30	0.00	1.40
3016	4414	0.756294	TGCTGGTTCTTCTCGGTTGA	59.244	50.000	0.00	0.00	0.00	3.18
3032	4430	3.627395	TTCGATGTTGGAGGTTATGCT	57.373	42.857	0.00	0.00	0.00	3.79
3352	4751	3.708631	AGGGAGTCAAGATCGTCATCATT	59.291	43.478	0.00	0.00	0.00	2.57
3509	4908	4.783764	TCACGAAGAGATCAAGTGCTTA	57.216	40.909	0.00	0.00	33.28	3.09

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.