AutoCloner

Multiple sequence alignment - TraesCS2D01G197900

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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	TraesCS2D01G197900	chr2D	100.000	2597	0	0	1	2597	145672047	145674643	0.000000e+00	4796.0
1	TraesCS2D01G197900	chr2D	80.480	333	29	17	369	691	348608113	348607807	3.360000e-54	222.0
2	TraesCS2D01G197900	chr2D	91.304	161	14	0	1902	2062	74967400	74967560	1.210000e-53	220.0
3	TraesCS2D01G197900	chr2D	84.375	96	13	2	708	802	199128432	199128338	2.750000e-15	93.5
4	TraesCS2D01G197900	chr2B	96.978	1092	27	3	698	1784	205480438	205479348	0.000000e+00	1829.0
5	TraesCS2D01G197900	chr2B	88.189	508	45	9	168	670	205481967	205481470	2.230000e-165	592.0
6	TraesCS2D01G197900	chr2B	87.795	508	46	9	168	670	205533139	205532643	4.820000e-162	580.0
7	TraesCS2D01G197900	chr2B	95.751	353	14	1	2245	2597	205530268	205529917	3.750000e-158	568.0
8	TraesCS2D01G197900	chr2B	95.184	353	16	1	2245	2597	205479123	205478772	8.120000e-155	556.0
9	TraesCS2D01G197900	chr2B	94.690	226	11	1	1970	2195	205479351	205479127	1.480000e-92	350.0
10	TraesCS2D01G197900	chr2B	94.690	226	11	1	1970	2195	205530496	205530272	1.480000e-92	350.0
11	TraesCS2D01G197900	chr2B	95.946	148	6	0	1637	1784	205530640	205530493	9.290000e-60	241.0
12	TraesCS2D01G197900	chr2B	90.184	163	16	0	1902	2064	114061708	114061870	2.020000e-51	213.0
13	TraesCS2D01G197900	chr2B	96.078	102	4	0	1549	1650	205530762	205530661	1.600000e-37	167.0
14	TraesCS2D01G197900	chr2B	93.939	66	3	1	100	165	205501458	205501394	5.910000e-17	99.0
15	TraesCS2D01G197900	chr2B	93.939	66	3	1	100	165	205552671	205552607	5.910000e-17	99.0
16	TraesCS2D01G197900	chr2A	89.706	1224	72	33	871	2064	156527363	156526164	0.000000e+00	1513.0
17	TraesCS2D01G197900	chr2A	90.175	916	54	16	1	882	156528820	156527907	0.000000e+00	1160.0
18	TraesCS2D01G197900	chr2A	88.957	163	18	0	1902	2064	74137388	74137550	4.380000e-48	202.0
19	TraesCS2D01G197900	chr2A	86.364	176	16	7	516	688	566473833	566473663	4.410000e-43	185.0
20	TraesCS2D01G197900	chr2A	87.755	98	9	3	712	808	196321123	196321028	7.600000e-21	111.0
21	TraesCS2D01G197900	chr2A	87.500	96	9	3	712	806	196347055	196346962	9.830000e-20	108.0
22	TraesCS2D01G197900	chr2A	85.859	99	11	3	712	809	196328762	196328666	4.570000e-18	102.0
23	TraesCS2D01G197900	chr5B	83.533	334	37	10	374	689	24423946	24424279	1.950000e-76	296.0
24	TraesCS2D01G197900	chr5B	83.439	314	36	8	392	689	6681233	6681546	7.080000e-71	278.0
25	TraesCS2D01G197900	chr3A	83.540	322	30	12	379	691	225892123	225891816	1.970000e-71	279.0
26	TraesCS2D01G197900	chr3A	89.773	88	9	0	721	808	505035501	505035414	2.110000e-21	113.0
27	TraesCS2D01G197900	chr1B	82.201	309	34	14	395	691	176284876	176284577	2.000000e-61	246.0
28	TraesCS2D01G197900	chr1B	89.441	161	17	0	1902	2062	631230136	631230296	1.220000e-48	204.0
29	TraesCS2D01G197900	chr7A	81.288	326	31	15	374	689	426559404	426559709	1.200000e-58	237.0
30	TraesCS2D01G197900	chr7A	79.245	318	29	12	367	673	573678588	573678297	1.230000e-43	187.0
31	TraesCS2D01G197900	chr1A	80.240	334	43	15	369	691	513381543	513381864	2.010000e-56	230.0
32	TraesCS2D01G197900	chr1A	90.062	161	16	0	1902	2062	551485577	551485737	2.620000e-50	209.0
33	TraesCS2D01G197900	chr1A	81.481	270	32	9	369	623	60582662	60582396	3.390000e-49	206.0
34	TraesCS2D01G197900	chr7B	79.755	326	43	18	369	683	23408322	23408635	5.630000e-52	215.0
35	TraesCS2D01G197900	chr1D	90.062	161	16	0	1902	2062	459050942	459051102	2.620000e-50	209.0
36	TraesCS2D01G197900	chr4A	79.758	331	32	14	369	691	306968680	306968377	9.420000e-50	207.0
37	TraesCS2D01G197900	chr4A	86.735	98	10	3	712	808	456416308	456416213	3.530000e-19	106.0
38	TraesCS2D01G197900	chr4A	86.735	98	10	3	712	808	586679498	586679403	3.530000e-19	106.0

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	TraesCS2D01G197900	chr2D	145672047	145674643	2596	False	4796.00	4796	100.00000	1	2597	1	chr2D.!!$F2	2596
1	TraesCS2D01G197900	chr2B	205478772	205481967	3195	True	831.75	1829	93.76025	168	2597	4	chr2B.!!$R3	2429
2	TraesCS2D01G197900	chr2B	205529917	205533139	3222	True	381.20	580	94.05200	168	2597	5	chr2B.!!$R4	2429
3	TraesCS2D01G197900	chr2A	156526164	156528820	2656	True	1336.50	1513	89.94050	1	2064	2	chr2A.!!$R5	2063

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
750	1772	0.035439	CTAAACATGTCGGTGGGCCT	60.035	55.0	4.53	0.0	0.0	5.19	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1875	3535	0.036732	CAGCCAGCAGTTTGGTAGGA	59.963	55.0	0.0	0.0	40.49	2.94	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
32	33	5.565834	GCCTAGCTATCCTATCACTGTTGTC	60.566	48.000	0.00	0.00	0.00	3.18
38	39	4.672587	TCCTATCACTGTTGTCTATGGC	57.327	45.455	0.00	0.00	0.00	4.40
91	92	3.679980	GCGAGTGAGTCATTTCTTGCTTA	59.320	43.478	12.21	0.00	35.27	3.09
154	156	9.283768	TGCTCTATTTTTCTAATCTTGTGTGAA	57.716	29.630	0.00	0.00	0.00	3.18
165	167	2.126467	CTTGTGTGAAAACAATGGCGG	58.874	47.619	0.00	0.00	39.25	6.13
209	211	4.825252	GCCCGATAACCCACGCGT	62.825	66.667	5.58	5.58	0.00	6.01
232	234	1.447217	CCGTGATGAGCATGGCCTA	59.553	57.895	3.32	0.00	46.16	3.93
239	241	0.391130	TGAGCATGGCCTAACACGTC	60.391	55.000	3.32	0.00	0.00	4.34
249	251	2.159338	GCCTAACACGTCTACAATCGGA	60.159	50.000	0.00	0.00	0.00	4.55
408	413	5.472320	TGTAAACACACATACACACACAC	57.528	39.130	0.00	0.00	0.00	3.82
488	494	8.538701	AGACAAATATGTATTTTCAAATGGGCA	58.461	29.630	0.00	0.00	40.74	5.36
491	497	9.381033	CAAATATGTATTTTCAAATGGGCAAGA	57.619	29.630	0.00	0.00	33.88	3.02
529	536	5.592688	GGGCCAGATATTTTGTACAGCTTAA	59.407	40.000	4.39	0.00	0.00	1.85
575	584	6.419484	AATCATGGATCCGTAGTGAATACA	57.581	37.500	6.04	0.00	33.65	2.29
586	595	7.037438	TCCGTAGTGAATACATACAAGTTTCC	58.963	38.462	0.00	0.00	33.65	3.13
591	600	6.149474	AGTGAATACATACAAGTTTCCACAGC	59.851	38.462	0.00	0.00	0.00	4.40
595	604	5.125100	ACATACAAGTTTCCACAGCATTG	57.875	39.130	0.00	0.00	0.00	2.82
600	609	5.244755	ACAAGTTTCCACAGCATTGTTTTT	58.755	33.333	0.00	0.00	34.62	1.94
706	1707	4.694987	CACCCCGCCCCCAAACAT	62.695	66.667	0.00	0.00	0.00	2.71
750	1772	0.035439	CTAAACATGTCGGTGGGCCT	60.035	55.000	4.53	0.00	0.00	5.19
875	2452	2.289444	CCAGGTCTGTGTGAAACGGTAT	60.289	50.000	0.00	0.00	42.39	2.73
1572	3153	4.329392	CCATGCTGATCTACATTGGCATA	58.671	43.478	0.00	0.00	38.16	3.14
1624	3205	2.159085	CCGGATCCAGTAACTCCACTTC	60.159	54.545	13.41	0.00	0.00	3.01
1634	3215	1.800805	ACTCCACTTCATGCTTCGTG	58.199	50.000	0.00	0.00	0.00	4.35
1645	3260	2.686558	TGCTTCGTGTGCATTTTCTC	57.313	45.000	0.00	0.00	35.31	2.87
1750	3366	1.177668	GCGTCTGTGTACGTGTATCG	58.822	55.000	0.00	0.00	44.64	2.92
1765	3381	4.181578	GTGTATCGGTGTGTCTATGCTTT	58.818	43.478	0.00	0.00	0.00	3.51
1788	3448	5.499139	TGTTCTTGGTGTTCTTTAGCTTG	57.501	39.130	0.00	0.00	0.00	4.01
1799	3459	7.298854	GTGTTCTTTAGCTTGATTACCTTGAC	58.701	38.462	0.00	0.00	0.00	3.18
1801	3461	7.719633	TGTTCTTTAGCTTGATTACCTTGACTT	59.280	33.333	0.00	0.00	0.00	3.01
1805	3465	9.220767	CTTTAGCTTGATTACCTTGACTTACTT	57.779	33.333	0.00	0.00	0.00	2.24
1806	3466	9.569122	TTTAGCTTGATTACCTTGACTTACTTT	57.431	29.630	0.00	0.00	0.00	2.66
1841	3501	5.835113	ACAGTTTGTAGTGATTTGCAAGT	57.165	34.783	0.00	0.00	0.00	3.16
1845	3505	5.127031	AGTTTGTAGTGATTTGCAAGTTGGT	59.873	36.000	4.75	0.00	0.00	3.67
1849	3509	4.223320	AGTGATTTGCAAGTTGGTAACG	57.777	40.909	4.75	0.00	42.51	3.18
1852	3512	2.853731	TTTGCAAGTTGGTAACGTGG	57.146	45.000	4.75	0.00	40.54	4.94
1862	3522	2.428491	TGGTAACGTGGTATGCAAAGG	58.572	47.619	0.00	0.00	42.51	3.11
1871	3531	3.699038	GTGGTATGCAAAGGCCAATCTAA	59.301	43.478	5.01	0.00	40.13	2.10
1872	3532	4.342092	GTGGTATGCAAAGGCCAATCTAAT	59.658	41.667	5.01	0.00	40.13	1.73
1873	3533	5.534654	GTGGTATGCAAAGGCCAATCTAATA	59.465	40.000	5.01	0.00	40.13	0.98
1874	3534	5.534654	TGGTATGCAAAGGCCAATCTAATAC	59.465	40.000	5.01	5.77	40.13	1.89
1875	3535	5.770162	GGTATGCAAAGGCCAATCTAATACT	59.230	40.000	5.01	0.00	40.13	2.12
1876	3536	6.072452	GGTATGCAAAGGCCAATCTAATACTC	60.072	42.308	5.01	0.00	40.13	2.59
1877	3537	4.207165	TGCAAAGGCCAATCTAATACTCC	58.793	43.478	5.01	0.00	40.13	3.85
1878	3538	4.079787	TGCAAAGGCCAATCTAATACTCCT	60.080	41.667	5.01	0.00	40.13	3.69
1879	3539	5.131977	TGCAAAGGCCAATCTAATACTCCTA	59.868	40.000	5.01	0.00	40.13	2.94
1880	3540	5.470437	GCAAAGGCCAATCTAATACTCCTAC	59.530	44.000	5.01	0.00	0.00	3.18
1881	3541	5.827326	AAGGCCAATCTAATACTCCTACC	57.173	43.478	5.01	0.00	0.00	3.18
1887	3547	6.483640	GCCAATCTAATACTCCTACCAAACTG	59.516	42.308	0.00	0.00	0.00	3.16
1888	3548	6.483640	CCAATCTAATACTCCTACCAAACTGC	59.516	42.308	0.00	0.00	0.00	4.40
1900	3560	2.224113	ACCAAACTGCTGGCTGAATTTG	60.224	45.455	6.47	7.30	40.45	2.32
1907	3567	1.938016	GCTGGCTGAATTTGTTGCCTG	60.938	52.381	0.00	0.00	45.11	4.85
1911	3571	1.615392	GCTGAATTTGTTGCCTGGTCT	59.385	47.619	0.00	0.00	0.00	3.85
1914	3574	3.295093	TGAATTTGTTGCCTGGTCTTCA	58.705	40.909	0.00	0.00	0.00	3.02
1918	3578	2.479566	TGTTGCCTGGTCTTCATCTC	57.520	50.000	0.00	0.00	0.00	2.75
1923	3583	2.309755	TGCCTGGTCTTCATCTCCAATT	59.690	45.455	0.00	0.00	0.00	2.32
1931	3591	5.994668	GGTCTTCATCTCCAATTAGATCCAC	59.005	44.000	0.00	0.00	33.87	4.02
1952	3612	5.123027	CCACTAGAGCTGGAATGTTTTTCTC	59.877	44.000	0.00	0.00	0.00	2.87
1963	3623	5.990996	GGAATGTTTTTCTCTGCCAAATCAA	59.009	36.000	0.00	0.00	0.00	2.57
1995	3656	1.001378	ACAAACTTGGCAAGCTTAGCG	60.001	47.619	26.45	11.66	0.00	4.26
2070	3734	3.188460	ACCACTCGTTGCATTACATTGTC	59.812	43.478	0.00	0.00	0.00	3.18
2140	3804	4.778213	TCAGTTAAAGGGAGCTATGCAT	57.222	40.909	3.79	3.79	0.00	3.96
2163	3827	0.537143	TTGGCCAGCAATTCACGAGT	60.537	50.000	5.11	0.00	0.00	4.18
2167	3831	0.439985	CCAGCAATTCACGAGTGTCG	59.560	55.000	2.97	0.00	46.93	4.35
2169	3833	1.125021	CAGCAATTCACGAGTGTCGAC	59.875	52.381	9.11	9.11	43.74	4.20
2178	3842	1.080705	GAGTGTCGACCGGTCAAGG	60.081	63.158	32.80	17.73	37.30	3.61
2195	3859	7.416213	CCGGTCAAGGCTTGATAAAAATCATTA	60.416	37.037	30.70	2.78	42.47	1.90
2197	3861	9.822185	GGTCAAGGCTTGATAAAAATCATTAAT	57.178	29.630	30.70	0.00	42.47	1.40
2228	3892	9.504708	AAAAATCATTTAGAATCCATGCAACAA	57.495	25.926	0.00	0.00	0.00	2.83
2229	3893	9.504708	AAAATCATTTAGAATCCATGCAACAAA	57.495	25.926	0.00	0.00	0.00	2.83
2230	3894	9.675464	AAATCATTTAGAATCCATGCAACAAAT	57.325	25.926	0.00	0.00	0.00	2.32
2231	3895	9.675464	AATCATTTAGAATCCATGCAACAAATT	57.325	25.926	0.00	0.00	0.00	1.82
2232	3896	9.675464	ATCATTTAGAATCCATGCAACAAATTT	57.325	25.926	0.00	0.00	0.00	1.82
2233	3897	9.504708	TCATTTAGAATCCATGCAACAAATTTT	57.495	25.926	0.00	0.00	0.00	1.82
2387	4051	8.560374	AGAAGTCAAACATGTTTAAGAGCTTAC	58.440	33.333	22.87	14.17	0.00	2.34
2497	4161	0.323302	TACAAACATCGCCCTGCTCA	59.677	50.000	0.00	0.00	0.00	4.26
2563	4227	9.914131	TGAGTGAATCTAATTATCTTCGTATGG	57.086	33.333	0.00	0.00	0.00	2.74
2577	4241	6.010850	TCTTCGTATGGCTTATCTCTATGGT	58.989	40.000	0.00	0.00	0.00	3.55
2581	4245	5.279506	CGTATGGCTTATCTCTATGGTGGTT	60.280	44.000	0.00	0.00	0.00	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
24	25	0.036388	CCACCGCCATAGACAACAGT	60.036	55.000	0.00	0.00	0.00	3.55
27	28	0.958382	TTGCCACCGCCATAGACAAC	60.958	55.000	0.00	0.00	0.00	3.32
32	33	0.101040	CATGTTTGCCACCGCCATAG	59.899	55.000	0.00	0.00	0.00	2.23
38	39	3.876914	ACTATATGACATGTTTGCCACCG	59.123	43.478	0.00	0.00	0.00	4.94
91	92	9.768662	AAAAGCAAGAAATGACTCATTTTACAT	57.231	25.926	16.48	3.47	43.05	2.29
120	121	9.959721	AGATTAGAAAAATAGAGCAGGTTGTTA	57.040	29.630	0.00	0.00	0.00	2.41
121	122	8.870075	AGATTAGAAAAATAGAGCAGGTTGTT	57.130	30.769	0.00	0.00	0.00	2.83
154	156	0.321475	CCATTTGGCCGCCATTGTTT	60.321	50.000	14.30	0.00	31.53	2.83
232	234	1.731424	CGCTCCGATTGTAGACGTGTT	60.731	52.381	0.00	0.00	0.00	3.32
239	241	1.148157	CCAGCACGCTCCGATTGTAG	61.148	60.000	0.00	0.00	0.00	2.74
315	317	5.386958	AAGAAATAAGAAAGGAAACGGGC	57.613	39.130	0.00	0.00	0.00	6.13
425	430	7.362574	CCACGTGGGAAAGTAAAATGTAATGAT	60.363	37.037	27.57	0.00	40.01	2.45
549	556	7.773224	TGTATTCACTACGGATCCATGATTTTT	59.227	33.333	13.41	0.00	32.61	1.94
575	584	5.789643	AACAATGCTGTGGAAACTTGTAT	57.210	34.783	0.00	0.00	35.37	2.29
710	1711	1.508088	CACCAGCCCGCTTGATTTC	59.492	57.895	0.00	0.00	0.00	2.17
750	1772	2.010582	GCACAACAAGGAAACGGGCA	62.011	55.000	0.00	0.00	0.00	5.36
875	2452	4.340950	GCATATGCTTACCTAGGCCAAAAA	59.659	41.667	20.64	0.00	38.21	1.94
1425	3006	2.100631	CATCGTCAGGAACCCGCAC	61.101	63.158	0.00	0.00	0.00	5.34
1572	3153	0.896226	GGGTGAAGGCGTAGAAGACT	59.104	55.000	0.00	0.00	0.00	3.24
1645	3260	3.052745	ACAGACGCATAATCTACGCATG	58.947	45.455	0.00	0.00	0.00	4.06
1650	3265	4.973051	CAGACTGACAGACGCATAATCTAC	59.027	45.833	10.08	0.00	0.00	2.59
1750	3366	5.215160	CAAGAACAAAAGCATAGACACACC	58.785	41.667	0.00	0.00	0.00	4.16
1765	3381	5.650266	TCAAGCTAAAGAACACCAAGAACAA	59.350	36.000	0.00	0.00	0.00	2.83
1811	3471	8.020819	GCAAATCACTACAAACTGTAATTGCTA	58.979	33.333	0.00	0.00	31.67	3.49
1812	3472	6.863126	GCAAATCACTACAAACTGTAATTGCT	59.137	34.615	0.00	0.00	31.67	3.91
1813	3473	6.640499	TGCAAATCACTACAAACTGTAATTGC	59.360	34.615	0.00	0.00	34.22	3.56
1814	3474	8.572828	TTGCAAATCACTACAAACTGTAATTG	57.427	30.769	0.00	0.00	31.67	2.32
1816	3476	7.940850	ACTTGCAAATCACTACAAACTGTAAT	58.059	30.769	0.00	0.00	31.67	1.89
1818	3478	6.935741	ACTTGCAAATCACTACAAACTGTA	57.064	33.333	0.00	0.00	0.00	2.74
1820	3480	5.459762	CCAACTTGCAAATCACTACAAACTG	59.540	40.000	0.00	0.00	0.00	3.16
1821	3481	5.127031	ACCAACTTGCAAATCACTACAAACT	59.873	36.000	0.00	0.00	0.00	2.66
1822	3482	5.348164	ACCAACTTGCAAATCACTACAAAC	58.652	37.500	0.00	0.00	0.00	2.93
1824	3484	6.500041	GTTACCAACTTGCAAATCACTACAA	58.500	36.000	0.00	0.00	0.00	2.41
1826	3486	5.144359	CGTTACCAACTTGCAAATCACTAC	58.856	41.667	0.00	0.00	0.00	2.73
1827	3487	4.817464	ACGTTACCAACTTGCAAATCACTA	59.183	37.500	0.00	0.00	0.00	2.74
1828	3488	3.630312	ACGTTACCAACTTGCAAATCACT	59.370	39.130	0.00	0.00	0.00	3.41
1829	3489	3.728718	CACGTTACCAACTTGCAAATCAC	59.271	43.478	0.00	0.00	0.00	3.06
1841	3501	2.814919	CCTTTGCATACCACGTTACCAA	59.185	45.455	0.00	0.00	0.00	3.67
1845	3505	1.271434	TGGCCTTTGCATACCACGTTA	60.271	47.619	3.32	0.00	40.13	3.18
1849	3509	2.102578	AGATTGGCCTTTGCATACCAC	58.897	47.619	3.32	0.00	40.13	4.16
1852	3512	6.072452	GGAGTATTAGATTGGCCTTTGCATAC	60.072	42.308	3.32	4.02	40.13	2.39
1862	3522	6.483640	CAGTTTGGTAGGAGTATTAGATTGGC	59.516	42.308	0.00	0.00	0.00	4.52
1871	3531	2.092914	GCCAGCAGTTTGGTAGGAGTAT	60.093	50.000	0.00	0.00	40.49	2.12
1872	3532	1.278127	GCCAGCAGTTTGGTAGGAGTA	59.722	52.381	0.00	0.00	40.49	2.59
1873	3533	0.036875	GCCAGCAGTTTGGTAGGAGT	59.963	55.000	0.00	0.00	40.49	3.85
1874	3534	0.326264	AGCCAGCAGTTTGGTAGGAG	59.674	55.000	0.00	0.00	40.49	3.69
1875	3535	0.036732	CAGCCAGCAGTTTGGTAGGA	59.963	55.000	0.00	0.00	40.49	2.94
1876	3536	0.036732	TCAGCCAGCAGTTTGGTAGG	59.963	55.000	0.00	0.00	40.49	3.18
1877	3537	1.896220	TTCAGCCAGCAGTTTGGTAG	58.104	50.000	0.00	0.00	40.49	3.18
1878	3538	2.584835	ATTCAGCCAGCAGTTTGGTA	57.415	45.000	0.00	0.00	40.49	3.25
1879	3539	1.708341	AATTCAGCCAGCAGTTTGGT	58.292	45.000	0.00	0.00	40.49	3.67
1880	3540	2.224113	ACAAATTCAGCCAGCAGTTTGG	60.224	45.455	11.14	0.00	41.35	3.28
1881	3541	3.102052	ACAAATTCAGCCAGCAGTTTG	57.898	42.857	0.00	0.00	33.92	2.93
1887	3547	2.831597	GGCAACAAATTCAGCCAGC	58.168	52.632	0.00	0.00	46.26	4.85
1900	3560	1.003580	TGGAGATGAAGACCAGGCAAC	59.996	52.381	0.00	0.00	0.00	4.17
1907	3567	5.994668	GTGGATCTAATTGGAGATGAAGACC	59.005	44.000	0.00	0.00	36.27	3.85
1911	3571	7.256119	GCTCTAGTGGATCTAATTGGAGATGAA	60.256	40.741	11.26	0.00	36.27	2.57
1914	3574	6.211184	CAGCTCTAGTGGATCTAATTGGAGAT	59.789	42.308	11.26	0.00	38.94	2.75
1918	3578	4.590647	TCCAGCTCTAGTGGATCTAATTGG	59.409	45.833	0.00	0.00	39.28	3.16
1923	3583	4.809193	ACATTCCAGCTCTAGTGGATCTA	58.191	43.478	1.64	0.00	43.78	1.98
1931	3591	5.163774	GCAGAGAAAAACATTCCAGCTCTAG	60.164	44.000	0.00	0.00	30.74	2.43
2104	3768	8.674607	CCCTTTAACTGAATGTGAACCTTATAC	58.325	37.037	0.00	0.00	0.00	1.47
2140	3804	3.814625	TCGTGAATTGCTGGCCAATATA	58.185	40.909	7.01	0.00	43.22	0.86
2163	3827	2.504274	AAGCCTTGACCGGTCGACA	61.504	57.895	28.70	14.70	0.00	4.35
2167	3831	2.396590	TTATCAAGCCTTGACCGGTC	57.603	50.000	28.17	28.17	43.48	4.79
2169	3833	4.157656	TGATTTTTATCAAGCCTTGACCGG	59.842	41.667	9.77	0.00	43.48	5.28
2202	3866	9.504708	TTGTTGCATGGATTCTAAATGATTTTT	57.495	25.926	0.00	0.00	0.00	1.94
2203	3867	9.504708	TTTGTTGCATGGATTCTAAATGATTTT	57.495	25.926	0.00	0.00	0.00	1.82
2204	3868	9.675464	ATTTGTTGCATGGATTCTAAATGATTT	57.325	25.926	0.00	0.00	0.00	2.17
2205	3869	9.675464	AATTTGTTGCATGGATTCTAAATGATT	57.325	25.926	0.00	0.00	0.00	2.57
2206	3870	9.675464	AAATTTGTTGCATGGATTCTAAATGAT	57.325	25.926	0.00	0.00	0.00	2.45
2207	3871	9.504708	AAAATTTGTTGCATGGATTCTAAATGA	57.495	25.926	0.00	0.00	0.00	2.57
2232	3896	4.979943	TGCATGGATTATCTCGCAAAAA	57.020	36.364	0.00	0.00	0.00	1.94
2233	3897	4.157472	TGTTGCATGGATTATCTCGCAAAA	59.843	37.500	14.34	9.17	40.67	2.44
2234	3898	3.693578	TGTTGCATGGATTATCTCGCAAA	59.306	39.130	14.34	6.42	40.67	3.68
2235	3899	3.277715	TGTTGCATGGATTATCTCGCAA	58.722	40.909	10.61	10.61	37.05	4.85
2236	3900	2.916640	TGTTGCATGGATTATCTCGCA	58.083	42.857	0.00	0.00	0.00	5.10
2237	3901	3.969117	TTGTTGCATGGATTATCTCGC	57.031	42.857	0.00	0.00	0.00	5.03
2238	3902	6.497437	TGAAATTGTTGCATGGATTATCTCG	58.503	36.000	0.00	0.00	0.00	4.04
2239	3903	7.977853	AGTTGAAATTGTTGCATGGATTATCTC	59.022	33.333	0.00	0.00	0.00	2.75
2240	3904	7.844009	AGTTGAAATTGTTGCATGGATTATCT	58.156	30.769	0.00	0.00	0.00	1.98
2241	3905	7.760794	TGAGTTGAAATTGTTGCATGGATTATC	59.239	33.333	0.00	0.00	0.00	1.75
2242	3906	7.613585	TGAGTTGAAATTGTTGCATGGATTAT	58.386	30.769	0.00	0.00	0.00	1.28
2243	3907	6.990798	TGAGTTGAAATTGTTGCATGGATTA	58.009	32.000	0.00	0.00	0.00	1.75
2298	3962	0.835941	CTCCATGCCTCCAGCTAACT	59.164	55.000	0.00	0.00	44.23	2.24
2364	4028	6.704493	TCGTAAGCTCTTAAACATGTTTGACT	59.296	34.615	29.72	17.27	33.56	3.41
2525	4189	3.266772	AGATTCACTCAAAGGGCCATACA	59.733	43.478	6.18	0.00	0.00	2.29
2533	4197	9.319143	ACGAAGATAATTAGATTCACTCAAAGG	57.681	33.333	11.10	0.00	0.00	3.11
2563	4227	7.475137	AGAGATAACCACCATAGAGATAAGC	57.525	40.000	0.00	0.00	0.00	3.09
2569	4233	5.304101	AGCTCAAGAGATAACCACCATAGAG	59.696	44.000	0.32	0.00	0.00	2.43
2570	4234	5.211973	AGCTCAAGAGATAACCACCATAGA	58.788	41.667	0.32	0.00	0.00	1.98
2574	4238	5.537300	GATAGCTCAAGAGATAACCACCA	57.463	43.478	0.32	0.00	32.61	4.17

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.