AutoCloner

Multiple sequence alignment - TraesCS5D01G144800

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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	TraesCS5D01G144800	chr5D	100.000	3471	0	0	1	3471	231353576	231350106	0.000000e+00	6410
1	TraesCS5D01G144800	chr5D	89.093	871	65	12	2601	3469	252174203	252175045	0.000000e+00	1055
2	TraesCS5D01G144800	chr5D	86.145	166	7	9	2459	2609	535266876	535266712	7.710000e-37	165
3	TraesCS5D01G144800	chr5A	95.075	2457	80	22	71	2511	325930884	325933315	0.000000e+00	3829
4	TraesCS5D01G144800	chr5B	95.090	1955	64	11	660	2609	275033177	275035104	0.000000e+00	3049
5	TraesCS5D01G144800	chr5B	86.201	616	60	18	71	673	275032317	275032920	0.000000e+00	643
6	TraesCS5D01G144800	chr6D	96.636	862	28	1	2610	3471	220921845	220922705	0.000000e+00	1430
7	TraesCS5D01G144800	chr6D	95.829	863	35	1	2609	3471	235833489	235832628	0.000000e+00	1393
8	TraesCS5D01G144800	chr6D	90.023	872	55	10	2602	3471	120061053	120061894	0.000000e+00	1099
9	TraesCS5D01G144800	chr6D	85.207	169	9	8	2456	2609	212696284	212696451	3.590000e-35	159
10	TraesCS5D01G144800	chr3D	96.412	864	30	1	2608	3471	166870361	166869499	0.000000e+00	1423
11	TraesCS5D01G144800	chr3D	89.805	873	57	11	2604	3471	483059743	483058898	0.000000e+00	1090
12	TraesCS5D01G144800	chr3D	89.078	879	75	19	2607	3469	188781128	188780255	0.000000e+00	1072
13	TraesCS5D01G144800	chr3D	85.207	169	9	8	2456	2609	207581657	207581824	3.590000e-35	159
14	TraesCS5D01G144800	chr1D	95.528	872	38	1	2600	3471	112328944	112329814	0.000000e+00	1393
15	TraesCS5D01G144800	chr1D	93.757	865	51	3	2607	3471	483617145	483618006	0.000000e+00	1295
16	TraesCS5D01G144800	chr1D	92.661	872	37	7	2600	3471	375592360	375593204	0.000000e+00	1230
17	TraesCS5D01G144800	chr1D	92.175	869	40	7	2606	3471	355976371	355977214	0.000000e+00	1203
18	TraesCS5D01G144800	chr1D	90.438	868	55	9	2603	3469	131017095	131017935	0.000000e+00	1118
19	TraesCS5D01G144800	chr1D	84.615	169	10	8	2456	2609	91722023	91722190	1.670000e-33	154
20	TraesCS5D01G144800	chr7D	95.486	864	37	2	2610	3471	258191776	258192639	0.000000e+00	1378
21	TraesCS5D01G144800	chr7D	91.811	867	63	8	2610	3471	90501315	90500452	0.000000e+00	1201
22	TraesCS5D01G144800	chr7D	85.119	168	10	8	2456	2609	470405485	470405651	1.290000e-34	158
23	TraesCS5D01G144800	chr4A	85.403	1329	184	8	1014	2339	476979050	476980371	0.000000e+00	1371
24	TraesCS5D01G144800	chr4D	84.928	1327	194	4	1014	2339	99162703	99161382	0.000000e+00	1338
25	TraesCS5D01G144800	chr4D	94.329	864	44	5	2610	3471	359411452	359410592	0.000000e+00	1319
26	TraesCS5D01G144800	chr4D	94.118	595	32	3	2601	3194	458948148	458948740	0.000000e+00	902
27	TraesCS5D01G144800	chr4B	82.021	1613	252	20	751	2339	141429202	141427604	0.000000e+00	1338
28	TraesCS5D01G144800	chr4B	85.542	166	8	8	2459	2609	366392356	366392192	3.590000e-35	159
29	TraesCS5D01G144800	chr2D	90.230	870	54	12	2602	3469	410277167	410276327	0.000000e+00	1107
30	TraesCS5D01G144800	chr6B	85.542	166	8	8	2459	2609	10696454	10696290	3.590000e-35	159

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	TraesCS5D01G144800	chr5D	231350106	231353576	3470	True	6410	6410	100.0000	1	3471	1	chr5D.!!$R1	3470
1	TraesCS5D01G144800	chr5D	252174203	252175045	842	False	1055	1055	89.0930	2601	3469	1	chr5D.!!$F1	868
2	TraesCS5D01G144800	chr5A	325930884	325933315	2431	False	3829	3829	95.0750	71	2511	1	chr5A.!!$F1	2440
3	TraesCS5D01G144800	chr5B	275032317	275035104	2787	False	1846	3049	90.6455	71	2609	2	chr5B.!!$F1	2538
4	TraesCS5D01G144800	chr6D	220921845	220922705	860	False	1430	1430	96.6360	2610	3471	1	chr6D.!!$F3	861
5	TraesCS5D01G144800	chr6D	235832628	235833489	861	True	1393	1393	95.8290	2609	3471	1	chr6D.!!$R1	862
6	TraesCS5D01G144800	chr6D	120061053	120061894	841	False	1099	1099	90.0230	2602	3471	1	chr6D.!!$F1	869
7	TraesCS5D01G144800	chr3D	166869499	166870361	862	True	1423	1423	96.4120	2608	3471	1	chr3D.!!$R1	863
8	TraesCS5D01G144800	chr3D	483058898	483059743	845	True	1090	1090	89.8050	2604	3471	1	chr3D.!!$R3	867
9	TraesCS5D01G144800	chr3D	188780255	188781128	873	True	1072	1072	89.0780	2607	3469	1	chr3D.!!$R2	862
10	TraesCS5D01G144800	chr1D	112328944	112329814	870	False	1393	1393	95.5280	2600	3471	1	chr1D.!!$F2	871
11	TraesCS5D01G144800	chr1D	483617145	483618006	861	False	1295	1295	93.7570	2607	3471	1	chr1D.!!$F6	864
12	TraesCS5D01G144800	chr1D	375592360	375593204	844	False	1230	1230	92.6610	2600	3471	1	chr1D.!!$F5	871
13	TraesCS5D01G144800	chr1D	355976371	355977214	843	False	1203	1203	92.1750	2606	3471	1	chr1D.!!$F4	865
14	TraesCS5D01G144800	chr1D	131017095	131017935	840	False	1118	1118	90.4380	2603	3469	1	chr1D.!!$F3	866
15	TraesCS5D01G144800	chr7D	258191776	258192639	863	False	1378	1378	95.4860	2610	3471	1	chr7D.!!$F1	861
16	TraesCS5D01G144800	chr7D	90500452	90501315	863	True	1201	1201	91.8110	2610	3471	1	chr7D.!!$R1	861
17	TraesCS5D01G144800	chr4A	476979050	476980371	1321	False	1371	1371	85.4030	1014	2339	1	chr4A.!!$F1	1325
18	TraesCS5D01G144800	chr4D	99161382	99162703	1321	True	1338	1338	84.9280	1014	2339	1	chr4D.!!$R1	1325
19	TraesCS5D01G144800	chr4D	359410592	359411452	860	True	1319	1319	94.3290	2610	3471	1	chr4D.!!$R2	861
20	TraesCS5D01G144800	chr4D	458948148	458948740	592	False	902	902	94.1180	2601	3194	1	chr4D.!!$F1	593
21	TraesCS5D01G144800	chr4B	141427604	141429202	1598	True	1338	1338	82.0210	751	2339	1	chr4B.!!$R1	1588
22	TraesCS5D01G144800	chr2D	410276327	410277167	840	True	1107	1107	90.2300	2602	3469	1	chr2D.!!$R1	867

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
52	53	0.179043	GGAGGGGGCTTTTCTCGATC	60.179	60.0	0.0	0.0	0.0	3.69	F
1168	1476	0.397941	TGGACAAGGAGAAGGTGCTG	59.602	55.0	0.0	0.0	0.0	4.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1881	2204	0.179032	TGTTGGAACAGCATCCGTGT	60.179	50.0	0.00	0.0	46.59	4.49	R
3018	3351	0.179067	GACGGCGGGTCAATAATGGA	60.179	55.0	13.24	0.0	45.36	3.41	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
17	18	2.744709	ATTGGGTTTCGCCGTCGG	60.745	61.111	6.99	6.99	38.44	4.79
18	19	3.540367	ATTGGGTTTCGCCGTCGGT	62.540	57.895	13.94	0.00	38.44	4.69
19	20	4.668118	TGGGTTTCGCCGTCGGTC	62.668	66.667	13.94	4.36	38.44	4.79
33	34	4.712425	GGTCCGTGACCGTCCGTG	62.712	72.222	7.23	0.00	43.14	4.94
34	35	4.712425	GTCCGTGACCGTCCGTGG	62.712	72.222	0.00	0.00	0.00	4.94
35	36	4.953010	TCCGTGACCGTCCGTGGA	62.953	66.667	0.00	0.00	0.00	4.02
36	37	4.415332	CCGTGACCGTCCGTGGAG	62.415	72.222	0.00	0.00	0.00	3.86
37	38	4.415332	CGTGACCGTCCGTGGAGG	62.415	72.222	1.60	1.60	42.97	4.30
44	45	3.647771	GTCCGTGGAGGGGGCTTT	61.648	66.667	0.00	0.00	41.52	3.51
45	46	2.856988	TCCGTGGAGGGGGCTTTT	60.857	61.111	0.00	0.00	41.52	2.27
46	47	2.361230	CCGTGGAGGGGGCTTTTC	60.361	66.667	0.00	0.00	35.97	2.29
47	48	2.757077	CGTGGAGGGGGCTTTTCT	59.243	61.111	0.00	0.00	0.00	2.52
48	49	1.377333	CGTGGAGGGGGCTTTTCTC	60.377	63.158	0.00	0.00	0.00	2.87
49	50	1.377333	GTGGAGGGGGCTTTTCTCG	60.377	63.158	0.00	0.00	0.00	4.04
50	51	1.537889	TGGAGGGGGCTTTTCTCGA	60.538	57.895	0.00	0.00	0.00	4.04
51	52	0.914417	TGGAGGGGGCTTTTCTCGAT	60.914	55.000	0.00	0.00	0.00	3.59
52	53	0.179043	GGAGGGGGCTTTTCTCGATC	60.179	60.000	0.00	0.00	0.00	3.69
53	54	0.530870	GAGGGGGCTTTTCTCGATCG	60.531	60.000	9.36	9.36	0.00	3.69
54	55	2.180862	GGGGGCTTTTCTCGATCGC	61.181	63.158	11.09	0.00	0.00	4.58
55	56	1.153349	GGGGCTTTTCTCGATCGCT	60.153	57.895	11.09	0.00	0.00	4.93
56	57	1.432270	GGGGCTTTTCTCGATCGCTG	61.432	60.000	11.09	5.91	0.00	5.18
57	58	0.741221	GGGCTTTTCTCGATCGCTGT	60.741	55.000	11.09	0.00	0.00	4.40
58	59	1.079503	GGCTTTTCTCGATCGCTGTT	58.920	50.000	11.09	0.00	0.00	3.16
59	60	1.201965	GGCTTTTCTCGATCGCTGTTG	60.202	52.381	11.09	0.00	0.00	3.33
60	61	1.461127	GCTTTTCTCGATCGCTGTTGT	59.539	47.619	11.09	0.00	0.00	3.32
61	62	2.723010	GCTTTTCTCGATCGCTGTTGTG	60.723	50.000	11.09	0.00	0.00	3.33
62	63	0.790207	TTTCTCGATCGCTGTTGTGC	59.210	50.000	11.09	0.00	0.00	4.57
77	78	0.873721	TGTGCGTTGTGATGTGATGG	59.126	50.000	0.00	0.00	0.00	3.51
96	97	2.102084	TGGCGATGGATCTTCTTGAGAG	59.898	50.000	0.00	0.00	37.93	3.20
97	98	2.134346	GCGATGGATCTTCTTGAGAGC	58.866	52.381	0.00	0.00	40.09	4.09
120	121	1.982073	GAAAATCTCTGGCGTGCCGG	61.982	60.000	13.67	13.67	43.69	6.13
122	123	3.958147	AATCTCTGGCGTGCCGGTG	62.958	63.158	18.77	16.37	42.88	4.94
146	149	1.108776	CAGGGGCACATTGATTGGAG	58.891	55.000	0.00	0.00	0.00	3.86
183	186	2.167861	CCTTCTGTTCCGCGCTAGC	61.168	63.158	5.56	4.06	40.74	3.42
194	197	2.419198	CGCTAGCTCGCCCAGATT	59.581	61.111	13.93	0.00	0.00	2.40
195	198	1.227380	CGCTAGCTCGCCCAGATTT	60.227	57.895	13.93	0.00	0.00	2.17
196	199	0.811616	CGCTAGCTCGCCCAGATTTT	60.812	55.000	13.93	0.00	0.00	1.82
197	200	0.659957	GCTAGCTCGCCCAGATTTTG	59.340	55.000	7.70	0.00	0.00	2.44
198	201	1.743772	GCTAGCTCGCCCAGATTTTGA	60.744	52.381	7.70	0.00	0.00	2.69
199	202	2.843701	CTAGCTCGCCCAGATTTTGAT	58.156	47.619	0.00	0.00	0.00	2.57
200	203	2.134789	AGCTCGCCCAGATTTTGATT	57.865	45.000	0.00	0.00	0.00	2.57
212	215	7.525360	GCCCAGATTTTGATTTTTGGAGTTCTA	60.525	37.037	0.00	0.00	0.00	2.10
298	301	3.334691	TGCGGTCAGATTTCGAAATTCT	58.665	40.909	23.49	17.78	0.00	2.40
302	305	4.868171	CGGTCAGATTTCGAAATTCTACCA	59.132	41.667	29.26	14.62	0.00	3.25
358	364	3.871006	TCATTAGATGCACAAAGGTAGCG	59.129	43.478	0.00	0.00	0.00	4.26
520	530	1.139654	AGCGCTGCTGATGAAGGAATA	59.860	47.619	10.39	0.00	37.57	1.75
561	572	4.025040	TGAACTCTGAAATCCATGCAGT	57.975	40.909	0.00	0.00	0.00	4.40
735	1025	5.526111	TGTTACTTCTTTTTCAGGGAACTCG	59.474	40.000	0.00	0.00	40.21	4.18
796	1086	5.299148	AGATGTGCTTGCATAGAAGAGATC	58.701	41.667	0.00	0.00	0.00	2.75
883	1176	1.210931	CACCTTGCCTGCATCAACG	59.789	57.895	0.00	0.00	0.00	4.10
1051	1359	2.170607	CAGTGGGAAGATCGTAATGGGT	59.829	50.000	0.00	0.00	0.00	4.51
1061	1369	5.017490	AGATCGTAATGGGTAGGTATGAGG	58.983	45.833	0.00	0.00	0.00	3.86
1168	1476	0.397941	TGGACAAGGAGAAGGTGCTG	59.602	55.000	0.00	0.00	0.00	4.41
1207	1515	1.153549	GGTCAGGCGTGAGATCACC	60.154	63.158	9.83	3.84	43.66	4.02
1350	1658	2.922503	TGGCAAGCTCACCGAGGA	60.923	61.111	0.00	0.00	0.00	3.71
1359	1667	3.190849	CACCGAGGATGCTGCACG	61.191	66.667	3.57	3.64	0.00	5.34
1513	1821	2.738846	TGCACTTTCAGAATCGAAGAGC	59.261	45.455	0.00	8.53	43.63	4.09
1630	1938	0.741221	GGTCTTGCGGTGTCATCCTC	60.741	60.000	0.00	0.00	0.00	3.71
1633	1941	1.066858	TCTTGCGGTGTCATCCTCTTC	60.067	52.381	0.00	0.00	0.00	2.87
1881	2204	1.250328	CTGCCAAGTGAGAATGCCAA	58.750	50.000	0.00	0.00	0.00	4.52
1885	2208	1.069022	CCAAGTGAGAATGCCAACACG	60.069	52.381	0.00	0.00	38.15	4.49
1930	2253	1.569479	GGCGCAGGAAGAACAGTCAC	61.569	60.000	10.83	0.00	0.00	3.67
2372	2695	4.557705	AGCCTCAAGGGTAGCTTTAGATA	58.442	43.478	0.00	0.00	45.38	1.98
2398	2721	7.324935	TCTCACTTATTATGTTTAGTTCCGCA	58.675	34.615	0.00	0.00	0.00	5.69
2399	2722	7.820386	TCTCACTTATTATGTTTAGTTCCGCAA	59.180	33.333	0.00	0.00	0.00	4.85
2400	2723	7.745015	TCACTTATTATGTTTAGTTCCGCAAC	58.255	34.615	0.00	0.00	0.00	4.17
2401	2724	7.604927	TCACTTATTATGTTTAGTTCCGCAACT	59.395	33.333	0.00	0.00	45.39	3.16
2402	2725	8.234546	CACTTATTATGTTTAGTTCCGCAACTT	58.765	33.333	0.00	0.00	40.16	2.66
2514	2844	8.671384	TTGACAAGTAATAACTGTTGCTAAGT	57.329	30.769	2.69	0.21	35.62	2.24
2520	2850	7.676947	AGTAATAACTGTTGCTAAGTTGAGGA	58.323	34.615	2.69	0.00	38.32	3.71
2543	2873	6.071952	GGACATGGATTAAGCTGTTTCTTTGA	60.072	38.462	0.00	0.00	0.00	2.69
2642	2972	1.679305	ACGGCAGATGTCCTCGAGT	60.679	57.895	12.31	0.00	0.00	4.18
2658	2988	2.417933	TCGAGTTAGGACTTAGTCGTGC	59.582	50.000	16.60	9.78	35.88	5.34
2697	3027	2.108776	AGCTTAAAGGGGTTAAACGGGT	59.891	45.455	0.00	0.00	31.22	5.28
2756	3086	3.405831	GGTGAAGGTAAAAGCCTACGTT	58.594	45.455	0.00	0.00	38.03	3.99
2775	3105	3.432252	CGTTCAGTTGAGGTGGTATTGAC	59.568	47.826	0.00	0.00	0.00	3.18
2943	3274	2.759538	CGGCTCGGACTCTTAACTAG	57.240	55.000	0.00	0.00	0.00	2.57
3018	3351	0.831307	GCCATCTCCGGGTCTTAAGT	59.169	55.000	0.00	0.00	0.00	2.24
3152	3487	2.178580	GCCCCAGATTGATTTGAACCA	58.821	47.619	0.00	0.00	0.00	3.67
3183	3544	8.681486	TGTCAATCTTCAATTCTTTTGAGAGA	57.319	30.769	0.00	0.00	0.00	3.10

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1	2	4.238654	ACCGACGGCGAAACCCAA	62.239	61.111	15.16	0.00	40.82	4.12
17	18	4.712425	CCACGGACGGTCACGGAC	62.712	72.222	18.51	0.00	46.48	4.79
18	19	4.953010	TCCACGGACGGTCACGGA	62.953	66.667	18.51	13.62	46.48	4.69
19	20	4.415332	CTCCACGGACGGTCACGG	62.415	72.222	18.51	11.89	46.48	4.94
21	22	4.065281	CCCTCCACGGACGGTCAC	62.065	72.222	10.76	0.00	33.16	3.67
27	28	3.205851	AAAAGCCCCCTCCACGGAC	62.206	63.158	0.00	0.00	33.16	4.79
28	29	2.856988	AAAAGCCCCCTCCACGGA	60.857	61.111	0.00	0.00	33.16	4.69
29	30	2.361230	GAAAAGCCCCCTCCACGG	60.361	66.667	0.00	0.00	0.00	4.94
30	31	1.377333	GAGAAAAGCCCCCTCCACG	60.377	63.158	0.00	0.00	0.00	4.94
31	32	1.377333	CGAGAAAAGCCCCCTCCAC	60.377	63.158	0.00	0.00	0.00	4.02
32	33	0.914417	ATCGAGAAAAGCCCCCTCCA	60.914	55.000	0.00	0.00	0.00	3.86
33	34	0.179043	GATCGAGAAAAGCCCCCTCC	60.179	60.000	0.00	0.00	0.00	4.30
34	35	0.530870	CGATCGAGAAAAGCCCCCTC	60.531	60.000	10.26	0.00	0.00	4.30
35	36	1.522569	CGATCGAGAAAAGCCCCCT	59.477	57.895	10.26	0.00	0.00	4.79
36	37	2.180862	GCGATCGAGAAAAGCCCCC	61.181	63.158	21.57	0.00	0.00	5.40
37	38	1.153349	AGCGATCGAGAAAAGCCCC	60.153	57.895	21.57	0.00	0.00	5.80
38	39	0.741221	ACAGCGATCGAGAAAAGCCC	60.741	55.000	21.57	0.00	0.00	5.19
39	40	1.079503	AACAGCGATCGAGAAAAGCC	58.920	50.000	21.57	0.00	0.00	4.35
40	41	1.461127	ACAACAGCGATCGAGAAAAGC	59.539	47.619	21.57	0.00	0.00	3.51
41	42	2.723010	GCACAACAGCGATCGAGAAAAG	60.723	50.000	21.57	5.83	0.00	2.27
42	43	1.194547	GCACAACAGCGATCGAGAAAA	59.805	47.619	21.57	0.00	0.00	2.29
43	44	0.790207	GCACAACAGCGATCGAGAAA	59.210	50.000	21.57	0.00	0.00	2.52
44	45	2.445274	GCACAACAGCGATCGAGAA	58.555	52.632	21.57	0.00	0.00	2.87
45	46	4.169102	GCACAACAGCGATCGAGA	57.831	55.556	21.57	0.00	0.00	4.04
53	54	0.029300	ACATCACAACGCACAACAGC	59.971	50.000	0.00	0.00	0.00	4.40
54	55	1.330213	TCACATCACAACGCACAACAG	59.670	47.619	0.00	0.00	0.00	3.16
55	56	1.373570	TCACATCACAACGCACAACA	58.626	45.000	0.00	0.00	0.00	3.33
56	57	2.309693	CATCACATCACAACGCACAAC	58.690	47.619	0.00	0.00	0.00	3.32
57	58	1.266446	CCATCACATCACAACGCACAA	59.734	47.619	0.00	0.00	0.00	3.33
58	59	0.873721	CCATCACATCACAACGCACA	59.126	50.000	0.00	0.00	0.00	4.57
59	60	0.454957	GCCATCACATCACAACGCAC	60.455	55.000	0.00	0.00	0.00	5.34
60	61	1.875262	GCCATCACATCACAACGCA	59.125	52.632	0.00	0.00	0.00	5.24
61	62	1.226101	CGCCATCACATCACAACGC	60.226	57.895	0.00	0.00	0.00	4.84
62	63	1.009078	ATCGCCATCACATCACAACG	58.991	50.000	0.00	0.00	0.00	4.10
63	64	1.064505	CCATCGCCATCACATCACAAC	59.935	52.381	0.00	0.00	0.00	3.32
64	65	1.065564	TCCATCGCCATCACATCACAA	60.066	47.619	0.00	0.00	0.00	3.33
65	66	0.540923	TCCATCGCCATCACATCACA	59.459	50.000	0.00	0.00	0.00	3.58
66	67	1.802960	GATCCATCGCCATCACATCAC	59.197	52.381	0.00	0.00	0.00	3.06
67	68	1.695788	AGATCCATCGCCATCACATCA	59.304	47.619	0.00	0.00	0.00	3.07
68	69	2.469274	AGATCCATCGCCATCACATC	57.531	50.000	0.00	0.00	0.00	3.06
69	70	2.371179	AGAAGATCCATCGCCATCACAT	59.629	45.455	0.00	0.00	0.00	3.21
77	78	2.134346	GCTCTCAAGAAGATCCATCGC	58.866	52.381	0.00	0.00	32.19	4.58
96	97	1.135575	CACGCCAGAGATTTTCTTGGC	60.136	52.381	15.06	15.06	42.20	4.52
97	98	1.135575	GCACGCCAGAGATTTTCTTGG	60.136	52.381	0.00	0.00	32.41	3.61
98	99	1.135575	GGCACGCCAGAGATTTTCTTG	60.136	52.381	2.36	0.00	32.41	3.02
126	127	0.971959	TCCAATCAATGTGCCCCTGC	60.972	55.000	0.00	0.00	38.26	4.85
127	128	1.108776	CTCCAATCAATGTGCCCCTG	58.891	55.000	0.00	0.00	0.00	4.45
154	157	2.361230	CAGAAGGCCCCGGGTTTC	60.361	66.667	21.85	19.14	0.00	2.78
177	180	0.811616	AAAATCTGGGCGAGCTAGCG	60.812	55.000	12.91	1.09	38.18	4.26
183	186	3.928375	CCAAAAATCAAAATCTGGGCGAG	59.072	43.478	0.00	0.00	0.00	5.03
189	192	8.076178	ACGTAGAACTCCAAAAATCAAAATCTG	58.924	33.333	0.00	0.00	0.00	2.90
194	197	7.066525	AGACAACGTAGAACTCCAAAAATCAAA	59.933	33.333	0.00	0.00	0.00	2.69
195	198	6.540914	AGACAACGTAGAACTCCAAAAATCAA	59.459	34.615	0.00	0.00	0.00	2.57
196	199	6.018262	CAGACAACGTAGAACTCCAAAAATCA	60.018	38.462	0.00	0.00	0.00	2.57
197	200	6.363473	CAGACAACGTAGAACTCCAAAAATC	58.637	40.000	0.00	0.00	0.00	2.17
198	201	5.238650	CCAGACAACGTAGAACTCCAAAAAT	59.761	40.000	0.00	0.00	0.00	1.82
199	202	4.573201	CCAGACAACGTAGAACTCCAAAAA	59.427	41.667	0.00	0.00	0.00	1.94
200	203	4.124238	CCAGACAACGTAGAACTCCAAAA	58.876	43.478	0.00	0.00	0.00	2.44
212	215	2.470821	CGAGAGAAAACCAGACAACGT	58.529	47.619	0.00	0.00	0.00	3.99
241	244	5.130477	TGATTGGAAGATTGTACTACCTCCC	59.870	44.000	0.00	0.00	0.00	4.30
254	257	1.602311	GGCGCAGATGATTGGAAGAT	58.398	50.000	10.83	0.00	0.00	2.40
298	301	6.023603	AGGAGTCTTCCAGATAAACTTGGTA	58.976	40.000	0.00	0.00	46.64	3.25
302	305	4.534103	AGCAGGAGTCTTCCAGATAAACTT	59.466	41.667	0.00	0.00	46.64	2.66
318	321	1.751351	TGATTCGACACCTAGCAGGAG	59.249	52.381	8.91	4.08	37.67	3.69
358	364	3.483558	CGAAAGCAACAGAGAAAAACTGC	59.516	43.478	0.00	0.00	38.74	4.40
603	616	6.095440	GGATGGAAAGAAAATCGAATTCAGGA	59.905	38.462	14.46	0.00	0.00	3.86
735	1025	8.687824	TGAGACTTTGATTTCTTGTTTTTGAC	57.312	30.769	0.00	0.00	0.00	3.18
796	1086	4.327982	TGTTCTTGGTCTCACAGAAGAG	57.672	45.455	0.00	0.00	36.97	2.85
804	1094	2.705658	AGTGGTGATGTTCTTGGTCTCA	59.294	45.455	0.00	0.00	0.00	3.27
883	1176	2.109126	GGAGTCTGAATGGCGTGGC	61.109	63.158	0.00	0.00	0.00	5.01
1051	1359	3.051341	ACAATCTCCCCACCTCATACCTA	60.051	47.826	0.00	0.00	0.00	3.08
1061	1369	3.621558	CTTTCCCTAACAATCTCCCCAC	58.378	50.000	0.00	0.00	0.00	4.61
1359	1667	2.086869	TGAGCTGCTGGAAATACTTGC	58.913	47.619	7.01	0.00	0.00	4.01
1513	1821	0.681887	TGTGGAGCATGCCATCTTGG	60.682	55.000	15.66	0.00	40.68	3.61
1523	1831	3.580084	ACAGGTGGTGTGGAGCAT	58.420	55.556	0.00	0.00	38.28	3.79
1630	1938	3.303791	GGTAACCAGCAACAAGAACGAAG	60.304	47.826	0.00	0.00	0.00	3.79
1633	1941	2.218603	AGGTAACCAGCAACAAGAACG	58.781	47.619	0.00	0.00	37.17	3.95
1881	2204	0.179032	TGTTGGAACAGCATCCGTGT	60.179	50.000	0.00	0.00	46.59	4.49
1930	2253	4.436998	AGGGGCTTCGCGTCTTCG	62.437	66.667	5.77	0.00	40.37	3.79
2372	2695	7.985184	TGCGGAACTAAACATAATAAGTGAGAT	59.015	33.333	0.00	0.00	0.00	2.75
2402	2725	7.643764	CACAATTACTCGAGCTGAAAAGAAAAA	59.356	33.333	13.61	0.00	0.00	1.94
2407	2730	5.597813	ACACAATTACTCGAGCTGAAAAG	57.402	39.130	13.61	0.69	0.00	2.27
2445	2775	3.696281	TTGTGACAAAGAGCACACATG	57.304	42.857	0.00	0.00	43.97	3.21
2446	2776	4.924305	ATTTGTGACAAAGAGCACACAT	57.076	36.364	16.43	0.00	43.97	3.21
2447	2777	5.826601	TTATTTGTGACAAAGAGCACACA	57.173	34.783	16.43	0.00	43.97	3.72
2514	2844	4.574674	ACAGCTTAATCCATGTCCTCAA	57.425	40.909	0.00	0.00	0.00	3.02
2520	2850	6.899393	TCAAAGAAACAGCTTAATCCATGT	57.101	33.333	0.00	0.00	0.00	3.21
2642	2972	1.203994	GGCTGCACGACTAAGTCCTAA	59.796	52.381	0.50	0.00	0.00	2.69
2658	2988	0.879400	CTTCCTAGCTGCGATGGCTG	60.879	60.000	0.00	1.21	40.52	4.85
2697	3027	1.364269	ATAACCCCCGTGTTCCTTGA	58.636	50.000	0.00	0.00	0.00	3.02
2756	3086	5.104941	CCATAGTCAATACCACCTCAACTGA	60.105	44.000	0.00	0.00	0.00	3.41
2775	3105	4.615949	CTCTCTGGTCATCGAAACCATAG	58.384	47.826	19.82	20.34	45.47	2.23
2794	3124	2.289320	CCAGGCATAGCGATTAAGCTCT	60.289	50.000	0.00	0.00	45.67	4.09
2862	3193	5.364446	TGGGCGTCAACCTCTCTATATAAAA	59.636	40.000	0.00	0.00	0.00	1.52
2943	3274	4.451435	GGAACTTGTAGTGTAAGGCAAGAC	59.549	45.833	9.68	4.19	40.30	3.01
3018	3351	0.179067	GACGGCGGGTCAATAATGGA	60.179	55.000	13.24	0.00	45.36	3.41
3152	3487	9.472361	CAAAAGAATTGAAGATTGACATGAACT	57.528	29.630	0.00	0.00	0.00	3.01
3398	3794	1.517832	CGAGAAACGAGGAGGCCAT	59.482	57.895	5.01	0.00	45.77	4.40

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.