AutoCloner

Multiple sequence alignment - TraesCS7D01G396100

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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	TraesCS7D01G396100	chr7D	100.000	3294	0	0	1532	4825	510705004	510708297	0.000000e+00	6083.0
1	TraesCS7D01G396100	chr7D	100.000	1315	0	0	1	1315	510703473	510704787	0.000000e+00	2429.0
2	TraesCS7D01G396100	chr7D	93.125	160	11	0	610	769	510703242	510703083	8.070000e-58	235.0
3	TraesCS7D01G396100	chr7D	93.939	66	4	0	2792	2857	510706226	510706291	3.070000e-17	100.0
4	TraesCS7D01G396100	chr7D	93.939	66	4	0	2754	2819	510706264	510706329	3.070000e-17	100.0
5	TraesCS7D01G396100	chr7A	94.966	2900	80	23	1550	4422	581430119	581432979	0.000000e+00	4486.0
6	TraesCS7D01G396100	chr7A	87.679	560	35	16	764	1314	581429552	581430086	5.300000e-174	621.0
7	TraesCS7D01G396100	chr7A	84.857	350	15	12	4511	4825	581433020	581433366	7.790000e-83	318.0
8	TraesCS7D01G396100	chr7B	95.745	1316	46	8	2905	4214	539231544	539232855	0.000000e+00	2111.0
9	TraesCS7D01G396100	chr7B	93.645	1070	38	10	1550	2590	539230043	539231111	0.000000e+00	1572.0
10	TraesCS7D01G396100	chr7B	90.893	582	28	8	4253	4825	539232858	539233423	0.000000e+00	758.0
11	TraesCS7D01G396100	chr7B	84.926	544	38	19	772	1313	539229509	539230010	1.200000e-140	510.0
12	TraesCS7D01G396100	chr7B	93.860	114	7	0	2706	2819	539231338	539231451	6.420000e-39	172.0
13	TraesCS7D01G396100	chr7B	93.671	79	4	1	2802	2880	539231396	539231473	3.050000e-22	117.0
14	TraesCS7D01G396100	chr6D	91.772	790	40	12	1	769	429149339	429150124	0.000000e+00	1075.0
15	TraesCS7D01G396100	chr6D	77.125	800	155	22	3050	3826	131687405	131686611	5.730000e-119	438.0
16	TraesCS7D01G396100	chr6D	76.471	799	159	25	3050	3826	131679030	131678239	1.620000e-109	407.0
17	TraesCS7D01G396100	chr6D	93.548	155	10	0	609	763	429149104	429148950	1.040000e-56	231.0
18	TraesCS7D01G396100	chr6D	85.000	160	21	3	1880	2038	131688609	131688452	5.000000e-35	159.0
19	TraesCS7D01G396100	chr5A	88.116	791	71	7	1	770	14291504	14290716	0.000000e+00	918.0
20	TraesCS7D01G396100	chr5A	91.026	156	14	0	611	766	14291746	14291901	1.360000e-50	211.0
21	TraesCS7D01G396100	chr2B	80.548	694	81	34	84	769	766030937	766030290	7.260000e-133	484.0
22	TraesCS7D01G396100	chr2B	90.683	161	15	0	609	769	766031215	766031375	1.050000e-51	215.0
23	TraesCS7D01G396100	chr6A	76.779	801	158	23	3050	3827	170012053	170011258	1.610000e-114	424.0
24	TraesCS7D01G396100	chr6A	84.146	164	21	5	1880	2041	169989973	169989813	2.330000e-33	154.0
25	TraesCS7D01G396100	chr6A	84.472	161	20	5	1880	2038	170013214	170013057	2.330000e-33	154.0
26	TraesCS7D01G396100	chr6A	88.235	119	14	0	3708	3826	169973374	169973256	5.030000e-30	143.0
27	TraesCS7D01G396100	chr6A	100.000	48	0	0	4703	4750	39607552	39607505	6.650000e-14	89.8
28	TraesCS7D01G396100	chr6A	98.000	50	0	1	4702	4750	39566068	39566019	8.600000e-13	86.1
29	TraesCS7D01G396100	chr6A	98.000	50	0	1	4702	4750	63252134	63252085	8.600000e-13	86.1
30	TraesCS7D01G396100	chr6A	98.000	50	0	1	4702	4750	165864097	165864146	8.600000e-13	86.1
31	TraesCS7D01G396100	chr5D	94.444	270	13	2	3932	4201	390709879	390710146	9.660000e-112	414.0
32	TraesCS7D01G396100	chr5D	82.870	216	20	5	4620	4825	390738327	390738535	1.380000e-40	178.0
33	TraesCS7D01G396100	chr6B	76.095	799	162	26	3050	3826	229202238	229201447	1.630000e-104	390.0
34	TraesCS7D01G396100	chr6B	84.472	161	20	5	1880	2038	229206711	229206554	2.330000e-33	154.0
35	TraesCS7D01G396100	chr5B	89.456	294	16	5	3933	4224	471137883	471138163	1.650000e-94	357.0
36	TraesCS7D01G396100	chr5B	84.043	188	17	3	4646	4823	471138868	471139052	8.310000e-38	169.0
37	TraesCS7D01G396100	chr1B	85.802	162	21	2	610	770	465248333	465248493	2.310000e-38	171.0
38	TraesCS7D01G396100	chr4D	77.953	254	49	7	522	769	402523558	402523306	8.360000e-33	152.0
39	TraesCS7D01G396100	chr4B	100.000	48	0	0	4703	4750	260433360	260433313	6.650000e-14	89.8
40	TraesCS7D01G396100	chr4B	79.825	114	23	0	392	505	667682451	667682564	3.090000e-12	84.2

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	TraesCS7D01G396100	chr7D	510703473	510708297	4824	False	2178.000000	6083	96.969500	1	4825	4	chr7D.!!$F1	4824
1	TraesCS7D01G396100	chr7A	581429552	581433366	3814	False	1808.333333	4486	89.167333	764	4825	3	chr7A.!!$F1	4061
2	TraesCS7D01G396100	chr7B	539229509	539233423	3914	False	873.333333	2111	92.123333	772	4825	6	chr7B.!!$F1	4053
3	TraesCS7D01G396100	chr6D	429149339	429150124	785	False	1075.000000	1075	91.772000	1	769	1	chr6D.!!$F1	768
4	TraesCS7D01G396100	chr6D	131678239	131679030	791	True	407.000000	407	76.471000	3050	3826	1	chr6D.!!$R1	776
5	TraesCS7D01G396100	chr6D	131686611	131688609	1998	True	298.500000	438	81.062500	1880	3826	2	chr6D.!!$R3	1946
6	TraesCS7D01G396100	chr5A	14290716	14291504	788	True	918.000000	918	88.116000	1	770	1	chr5A.!!$R1	769
7	TraesCS7D01G396100	chr2B	766030290	766030937	647	True	484.000000	484	80.548000	84	769	1	chr2B.!!$R1	685
8	TraesCS7D01G396100	chr6A	170011258	170013214	1956	True	289.000000	424	80.625500	1880	3827	2	chr6A.!!$R6	1947
9	TraesCS7D01G396100	chr6B	229201447	229202238	791	True	390.000000	390	76.095000	3050	3826	1	chr6B.!!$R1	776
10	TraesCS7D01G396100	chr5B	471137883	471139052	1169	False	263.000000	357	86.749500	3933	4823	2	chr5B.!!$F1	890

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
805	846	0.029700	GTTAAAAACGCCACGTGCCT	59.970	50.00	10.91	0.00	39.99	4.75	F
1183	1236	0.032815	GGATCTGGGAAGCGCTAGTC	59.967	60.00	12.05	5.19	0.00	2.59	F
1239	1292	0.034756	GGGTTTTGGTTGGTGGATGC	59.965	55.00	0.00	0.00	0.00	3.91	F
1261	1314	0.477597	TGGGGAAGATTGGGGTCTGT	60.478	55.00	0.00	0.00	0.00	3.41	F
2367	2545	2.096496	GGGAGCAATTGAGTGTTCATCG	59.904	50.00	10.34	0.00	32.27	3.84	F
3516	4238	4.397420	AGTCAACACAAAGCACATATCCA	58.603	39.13	0.00	0.00	0.00	3.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1775	1837	0.911769	TCCAGTACCCCAAGCAGATG	59.088	55.000	0.00	0.00	2.90	R
2432	2610	2.240921	TGCAAGTAGGTATGGCATTGGA	59.759	45.455	4.78	0.00	3.53	R
2778	3159	4.153655	TCTGATGTGTAGTGTACAGACGAC	59.846	45.833	0.00	39.77	4.34	R
3002	3722	6.790825	GCGAACTTACACAACAATCTAAACTC	59.209	38.462	0.00	0.00	3.01	R
3542	4264	0.759346	GGTCTGCCTCATTATCCCGT	59.241	55.000	0.00	0.00	5.28	R
4613	5662	1.900245	TGCTTTCAGCTGCTTGATCA	58.100	45.000	9.47	42.97	2.92	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
82	98	1.891919	GTGCAAGTTGTCCCGAGCA	60.892	57.895	4.48	0.00	0.00	4.26
152	168	2.203523	TGGTTGTCCTCGTCCGGA	60.204	61.111	0.00	0.00	34.23	5.14
211	227	1.227586	CCATGCATCGAGCTGCTCT	60.228	57.895	25.59	6.84	45.94	4.09
216	232	0.738762	GCATCGAGCTGCTCTGAACA	60.739	55.000	25.59	6.37	41.15	3.18
360	378	2.047274	CAGCGTGGGGTGGTGTAG	60.047	66.667	0.00	0.00	38.00	2.74
361	379	4.016706	AGCGTGGGGTGGTGTAGC	62.017	66.667	0.00	0.00	0.00	3.58
590	631	3.631144	CAAACAGTGCTAACATGTGTGG	58.369	45.455	0.00	0.00	30.06	4.17
600	641	1.073722	CATGTGTGGCAGGTGGACT	59.926	57.895	0.00	0.00	0.00	3.85
728	769	2.607499	AGAAATGTGGTGGCAATTCCA	58.393	42.857	0.00	0.00	44.18	3.53
805	846	0.029700	GTTAAAAACGCCACGTGCCT	59.970	50.000	10.91	0.00	39.99	4.75
826	867	0.541998	ACTAAACCTTTGCCCCAGCC	60.542	55.000	0.00	0.00	38.69	4.85
827	868	0.541764	CTAAACCTTTGCCCCAGCCA	60.542	55.000	0.00	0.00	38.69	4.75
881	928	1.685077	TGCTGCCTCCTCCTCTCTG	60.685	63.158	0.00	0.00	0.00	3.35
885	932	0.324183	TGCCTCCTCCTCTCTGTCTG	60.324	60.000	0.00	0.00	0.00	3.51
887	934	1.894978	GCCTCCTCCTCTCTGTCTGTT	60.895	57.143	0.00	0.00	0.00	3.16
901	948	2.431260	TGTTTCTACCGACGCCGC	60.431	61.111	0.00	0.00	0.00	6.53
902	949	3.184003	GTTTCTACCGACGCCGCC	61.184	66.667	0.00	0.00	0.00	6.13
903	950	4.440127	TTTCTACCGACGCCGCCC	62.440	66.667	0.00	0.00	0.00	6.13
1084	1131	2.183046	GAGGTGAGCAGCCTCGTC	59.817	66.667	5.65	0.00	42.46	4.20
1085	1132	3.691744	GAGGTGAGCAGCCTCGTCG	62.692	68.421	5.65	0.00	42.46	5.12
1092	1142	3.250323	CAGCCTCGTCGTCGCATG	61.250	66.667	0.00	0.00	36.96	4.06
1093	1143	4.498520	AGCCTCGTCGTCGCATGG	62.499	66.667	0.00	1.10	36.96	3.66
1114	1164	2.021457	CCTGGTTTCTGGTTTCGTTGT	58.979	47.619	0.00	0.00	0.00	3.32
1118	1168	2.294979	GTTTCTGGTTTCGTTGTCCCT	58.705	47.619	0.00	0.00	0.00	4.20
1119	1169	1.961793	TTCTGGTTTCGTTGTCCCTG	58.038	50.000	0.00	0.00	0.00	4.45
1120	1170	0.534203	TCTGGTTTCGTTGTCCCTGC	60.534	55.000	0.00	0.00	0.00	4.85
1121	1171	0.535102	CTGGTTTCGTTGTCCCTGCT	60.535	55.000	0.00	0.00	0.00	4.24
1122	1172	0.534203	TGGTTTCGTTGTCCCTGCTC	60.534	55.000	0.00	0.00	0.00	4.26
1123	1173	1.235281	GGTTTCGTTGTCCCTGCTCC	61.235	60.000	0.00	0.00	0.00	4.70
1124	1174	1.072505	TTTCGTTGTCCCTGCTCCC	59.927	57.895	0.00	0.00	0.00	4.30
1159	1212	0.952497	GGTTTTCGTTCCCGTCCCTC	60.952	60.000	0.00	0.00	35.01	4.30
1183	1236	0.032815	GGATCTGGGAAGCGCTAGTC	59.967	60.000	12.05	5.19	0.00	2.59
1202	1255	3.263941	GCTAAGTTGCGTGGGTGG	58.736	61.111	0.00	0.00	0.00	4.61
1203	1256	2.978018	GCTAAGTTGCGTGGGTGGC	61.978	63.158	0.00	0.00	0.00	5.01
1204	1257	2.666862	TAAGTTGCGTGGGTGGCG	60.667	61.111	0.00	0.00	0.00	5.69
1205	1258	3.463728	TAAGTTGCGTGGGTGGCGT	62.464	57.895	0.00	0.00	0.00	5.68
1239	1292	0.034756	GGGTTTTGGTTGGTGGATGC	59.965	55.000	0.00	0.00	0.00	3.91
1242	1295	1.272212	GTTTTGGTTGGTGGATGCGAT	59.728	47.619	0.00	0.00	0.00	4.58
1248	1301	1.857638	TTGGTGGATGCGATGGGGAA	61.858	55.000	0.00	0.00	0.00	3.97
1257	1310	1.922821	CGATGGGGAAGATTGGGGT	59.077	57.895	0.00	0.00	0.00	4.95
1261	1314	0.477597	TGGGGAAGATTGGGGTCTGT	60.478	55.000	0.00	0.00	0.00	3.41
1276	1329	2.418884	GGTCTGTTAGGAGCTTGTAGCC	60.419	54.545	0.00	0.00	43.77	3.93
1648	1710	6.649041	AATTATTAGCAGGATCTGGGCTAT	57.351	37.500	12.13	7.27	39.63	2.97
1663	1725	5.775701	TCTGGGCTATTATTCTGGTAGAGAC	59.224	44.000	0.00	0.00	0.00	3.36
1670	1732	6.827586	ATTATTCTGGTAGAGACGATCCTC	57.172	41.667	0.00	0.00	0.00	3.71
1775	1837	7.927048	ACTCCTAATTTAAATCGTTGGCATAC	58.073	34.615	0.10	0.00	0.00	2.39
1776	1838	7.554835	ACTCCTAATTTAAATCGTTGGCATACA	59.445	33.333	0.10	0.00	0.00	2.29
2159	2251	7.682787	ACTACAGGTTCCTCATCTAATTCAT	57.317	36.000	0.00	0.00	0.00	2.57
2252	2349	9.508567	GAAGAATGCAACAAGAATTATAAGGAC	57.491	33.333	0.00	0.00	0.00	3.85
2367	2545	2.096496	GGGAGCAATTGAGTGTTCATCG	59.904	50.000	10.34	0.00	32.27	3.84
2412	2590	9.857656	ATTGTTGATAATCCAGTATCAGTCATT	57.142	29.630	0.00	0.00	40.64	2.57
2419	2597	7.798596	AATCCAGTATCAGTCATTGATGTTC	57.201	36.000	0.00	0.00	46.01	3.18
2420	2598	5.674525	TCCAGTATCAGTCATTGATGTTCC	58.325	41.667	0.00	0.00	46.01	3.62
2432	2610	7.068839	AGTCATTGATGTTCCGACTATCTAGTT	59.931	37.037	0.00	0.00	36.50	2.24
2778	3159	6.100004	ACACATCAAACGTAGGATCTAAGTG	58.900	40.000	12.23	12.23	0.00	3.16
3001	3721	9.103861	TGCATTATAAATCATCAGTCGTGTTAA	57.896	29.630	0.00	0.00	0.00	2.01
3002	3722	9.586150	GCATTATAAATCATCAGTCGTGTTAAG	57.414	33.333	0.00	0.00	0.00	1.85
3516	4238	4.397420	AGTCAACACAAAGCACATATCCA	58.603	39.130	0.00	0.00	0.00	3.41
4020	4763	4.156556	CCGAGAATGGATTTGCTTTTGAGA	59.843	41.667	0.00	0.00	0.00	3.27
4152	4895	5.010112	TCTGGAGAGTTATAGAATCAAGCCG	59.990	44.000	0.00	0.00	0.00	5.52
4203	4946	1.002087	GTCAGTCTGGGACCGAACATT	59.998	52.381	0.00	0.00	32.18	2.71
4204	4947	2.232941	GTCAGTCTGGGACCGAACATTA	59.767	50.000	0.00	0.00	32.18	1.90
4224	4969	8.603242	ACATTATTGGTATTTAGAGTAAGCCG	57.397	34.615	0.00	0.00	0.00	5.52
4245	4990	7.489160	AGCCGAAATTTTATTATCTTTCACCC	58.511	34.615	0.00	0.00	0.00	4.61
4250	4995	9.817809	GAAATTTTATTATCTTTCACCCCCTTC	57.182	33.333	0.00	0.00	0.00	3.46
4251	4996	7.914427	ATTTTATTATCTTTCACCCCCTTCC	57.086	36.000	0.00	0.00	0.00	3.46
4252	4997	6.668133	TTTATTATCTTTCACCCCCTTCCT	57.332	37.500	0.00	0.00	0.00	3.36
4264	5009	4.656575	CACCCCCTTCCTTTTTCCTTTAAA	59.343	41.667	0.00	0.00	0.00	1.52
4282	5027	9.748708	TCCTTTAAATTTTGACAATGAACAGAG	57.251	29.630	0.00	0.00	0.00	3.35
4283	5028	8.490355	CCTTTAAATTTTGACAATGAACAGAGC	58.510	33.333	0.00	0.00	0.00	4.09
4364	5109	1.372582	CGTCCAGTCACCATCCAATG	58.627	55.000	0.00	0.00	0.00	2.82
4385	5130	7.962918	CCAATGTCGTTTAAGAAGACTTAATGG	59.037	37.037	0.00	0.00	44.59	3.16
4404	5149	9.443283	CTTAATGGATGAATCAAAAGAATCGAC	57.557	33.333	0.00	0.00	0.00	4.20
4421	5466	1.542547	CGACAACCCTAACAGTTGCCT	60.543	52.381	3.66	0.00	46.85	4.75
4471	5519	4.920112	CACCCGAACGTGGTGCCA	62.920	66.667	10.27	0.00	46.13	4.92
4528	5576	2.099405	CCATGGCGTAAATTGTTCCCT	58.901	47.619	0.00	0.00	0.00	4.20
4553	5601	2.535984	GTCCAGACGAGTGATAATTGCG	59.464	50.000	0.00	0.00	0.00	4.85
4604	5653	3.221771	TGGATGTTCTTGGTCAGTTTGG	58.778	45.455	0.00	0.00	0.00	3.28
4608	5657	3.909732	TGTTCTTGGTCAGTTTGGGATT	58.090	40.909	0.00	0.00	0.00	3.01
4609	5658	5.055265	TGTTCTTGGTCAGTTTGGGATTA	57.945	39.130	0.00	0.00	0.00	1.75
4610	5659	5.070001	TGTTCTTGGTCAGTTTGGGATTAG	58.930	41.667	0.00	0.00	0.00	1.73
4611	5660	4.993705	TCTTGGTCAGTTTGGGATTAGT	57.006	40.909	0.00	0.00	0.00	2.24
4612	5661	6.183361	TGTTCTTGGTCAGTTTGGGATTAGTA	60.183	38.462	0.00	0.00	0.00	1.82
4613	5662	6.636454	TCTTGGTCAGTTTGGGATTAGTAT	57.364	37.500	0.00	0.00	0.00	2.12
4614	5663	6.414732	TCTTGGTCAGTTTGGGATTAGTATG	58.585	40.000	0.00	0.00	0.00	2.39
4697	5902	2.704725	AATGCAGCAGTAAACCAACG	57.295	45.000	0.00	0.00	0.00	4.10
4793	6005	0.558712	TTGCCCACCCCTACAAAAGT	59.441	50.000	0.00	0.00	0.00	2.66
4794	6006	0.111639	TGCCCACCCCTACAAAAGTC	59.888	55.000	0.00	0.00	0.00	3.01
4795	6007	0.611062	GCCCACCCCTACAAAAGTCC	60.611	60.000	0.00	0.00	0.00	3.85

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
31	32	1.303561	TGCAGCTTCGGAATGGCTT	60.304	52.632	2.07	0.00	33.74	4.35
211	227	1.208535	CTACCCCTATGCCGTTGTTCA	59.791	52.381	0.00	0.00	0.00	3.18
216	232	1.129058	CTTCCTACCCCTATGCCGTT	58.871	55.000	0.00	0.00	0.00	4.44
298	314	3.083997	CTCCCCTTCCTGTCCCGG	61.084	72.222	0.00	0.00	0.00	5.73
578	619	1.167851	CCACCTGCCACACATGTTAG	58.832	55.000	0.00	0.00	0.00	2.34
590	631	0.389948	CGTAGGTCAAGTCCACCTGC	60.390	60.000	1.43	0.00	44.51	4.85
698	739	0.679640	CCACATTTCTTGGCCGCCTA	60.680	55.000	11.61	1.40	0.00	3.93
699	740	1.978617	CCACATTTCTTGGCCGCCT	60.979	57.895	11.61	0.00	0.00	5.52
770	811	0.317799	TAACGGTGCGCTCTGGTAAA	59.682	50.000	21.32	0.00	0.00	2.01
805	846	2.521126	GCTGGGGCAAAGGTTTAGTTA	58.479	47.619	0.00	0.00	38.54	2.24
829	870	2.892425	GAGAAGATGGGGTGCGCG	60.892	66.667	0.00	0.00	0.00	6.86
830	871	2.514824	GGAGAAGATGGGGTGCGC	60.515	66.667	0.00	0.00	0.00	6.09
831	872	2.202932	CGGAGAAGATGGGGTGCG	60.203	66.667	0.00	0.00	0.00	5.34
832	873	2.190578	CCGGAGAAGATGGGGTGC	59.809	66.667	0.00	0.00	0.00	5.01
881	928	1.069378	CGGCGTCGGTAGAAACAGAC	61.069	60.000	0.00	0.00	44.46	3.51
885	932	3.184003	GGCGGCGTCGGTAGAAAC	61.184	66.667	13.05	0.00	36.79	2.78
905	952	4.761058	TTCTCTCTCGCGGGGGCT	62.761	66.667	5.94	0.00	0.00	5.19
906	953	3.771160	TTTCTCTCTCGCGGGGGC	61.771	66.667	5.94	0.00	0.00	5.80
1084	1131	3.039202	GAAACCAGGCCATGCGACG	62.039	63.158	5.01	0.00	0.00	5.12
1085	1132	1.675641	AGAAACCAGGCCATGCGAC	60.676	57.895	5.01	0.00	0.00	5.19
1090	1137	1.632589	GAAACCAGAAACCAGGCCAT	58.367	50.000	5.01	0.00	0.00	4.40
1091	1138	0.821711	CGAAACCAGAAACCAGGCCA	60.822	55.000	5.01	0.00	0.00	5.36
1092	1142	0.822121	ACGAAACCAGAAACCAGGCC	60.822	55.000	0.00	0.00	0.00	5.19
1093	1143	1.029681	AACGAAACCAGAAACCAGGC	58.970	50.000	0.00	0.00	0.00	4.85
1159	1212	2.203126	GCTTCCCAGATCCGGCAG	60.203	66.667	0.00	0.00	0.00	4.85
1188	1241	4.868116	ACGCCACCCACGCAACTT	62.868	61.111	0.00	0.00	0.00	2.66
1200	1253	4.717629	CTTCTCGCCACGACGCCA	62.718	66.667	0.00	0.00	0.00	5.69
1239	1292	0.179018	GACCCCAATCTTCCCCATCG	60.179	60.000	0.00	0.00	0.00	3.84
1242	1295	0.477597	ACAGACCCCAATCTTCCCCA	60.478	55.000	0.00	0.00	0.00	4.96
1248	1301	1.840635	GCTCCTAACAGACCCCAATCT	59.159	52.381	0.00	0.00	0.00	2.40
1257	1310	2.497675	CTGGCTACAAGCTCCTAACAGA	59.502	50.000	0.00	0.00	41.99	3.41
1261	1314	0.541863	GGCTGGCTACAAGCTCCTAA	59.458	55.000	0.00	0.00	41.99	2.69
1276	1329	1.137404	CCGCGGAAATTTCAGGCTG	59.863	57.895	24.07	8.58	0.00	4.85
1563	1618	4.263639	ACATCTCCAGATCTTTGGAAGCAA	60.264	41.667	5.30	0.00	46.20	3.91
1564	1619	3.265221	ACATCTCCAGATCTTTGGAAGCA	59.735	43.478	5.30	0.00	46.20	3.91
1565	1620	3.626670	CACATCTCCAGATCTTTGGAAGC	59.373	47.826	5.30	0.00	46.20	3.86
1618	1674	2.582052	TCCTGCTAATAATTTGCCCCG	58.418	47.619	0.00	0.00	0.00	5.73
1648	1710	5.942961	AGAGGATCGTCTCTACCAGAATAA	58.057	41.667	12.13	0.00	41.86	1.40
1663	1725	6.591834	ACAACAGAACATTTAAGAGAGGATCG	59.408	38.462	0.00	0.00	42.67	3.69
1726	1788	4.765273	TCCGTGCTATATTTCTGCTTTGA	58.235	39.130	0.00	0.00	0.00	2.69
1775	1837	0.911769	TCCAGTACCCCAAGCAGATG	59.088	55.000	0.00	0.00	0.00	2.90
1776	1838	1.207791	CTCCAGTACCCCAAGCAGAT	58.792	55.000	0.00	0.00	0.00	2.90
2159	2251	6.899089	TCCACTGGATATTCATTCTTAAGCA	58.101	36.000	0.00	0.00	0.00	3.91
2252	2349	5.885230	TCCATCTGAAAGCAAGTTACATG	57.115	39.130	0.00	0.00	0.00	3.21
2388	2566	8.485392	TCAATGACTGATACTGGATTATCAACA	58.515	33.333	0.00	0.00	37.89	3.33
2407	2585	6.740110	ACTAGATAGTCGGAACATCAATGAC	58.260	40.000	0.00	0.00	0.00	3.06
2412	2590	5.198207	TGGAACTAGATAGTCGGAACATCA	58.802	41.667	0.00	0.00	34.99	3.07
2419	2597	3.069586	TGGCATTGGAACTAGATAGTCGG	59.930	47.826	0.00	0.00	34.99	4.79
2420	2598	4.322080	TGGCATTGGAACTAGATAGTCG	57.678	45.455	0.00	0.00	34.99	4.18
2432	2610	2.240921	TGCAAGTAGGTATGGCATTGGA	59.759	45.455	4.78	0.00	0.00	3.53
2703	2938	7.722728	ACAACCACAGATGCTTCATCATATATT	59.277	33.333	9.19	0.00	42.72	1.28
2778	3159	4.153655	TCTGATGTGTAGTGTACAGACGAC	59.846	45.833	0.00	0.00	39.77	4.34
2922	3591	8.256611	TCTATTTAGTTGAACAAGATGACAGC	57.743	34.615	0.00	0.00	0.00	4.40
3001	3721	7.307219	GCGAACTTACACAACAATCTAAACTCT	60.307	37.037	0.00	0.00	0.00	3.24
3002	3722	6.790825	GCGAACTTACACAACAATCTAAACTC	59.209	38.462	0.00	0.00	0.00	3.01
3470	4192	1.654220	CTTCCCAATAATGGCGCCG	59.346	57.895	23.90	5.77	46.09	6.46
3516	4238	1.000396	GCTTGGCCCCAGTCATTCT	60.000	57.895	0.00	0.00	0.00	2.40
3542	4264	0.759346	GGTCTGCCTCATTATCCCGT	59.241	55.000	0.00	0.00	0.00	5.28
4020	4763	9.162764	CGGCAATACACTAAGCCTATAATAAAT	57.837	33.333	0.00	0.00	44.85	1.40
4152	4895	6.366332	ACATCACACGAAAGATACTCAAGTTC	59.634	38.462	0.00	0.00	0.00	3.01
4203	4946	9.841295	AATTTCGGCTTACTCTAAATACCAATA	57.159	29.630	0.00	0.00	0.00	1.90
4204	4947	8.747538	AATTTCGGCTTACTCTAAATACCAAT	57.252	30.769	0.00	0.00	0.00	3.16
4224	4969	9.817809	GAAGGGGGTGAAAGATAATAAAATTTC	57.182	33.333	0.00	0.00	33.31	2.17
4245	4990	8.836413	GTCAAAATTTAAAGGAAAAAGGAAGGG	58.164	33.333	0.00	0.00	0.00	3.95
4264	5009	8.798859	ATAGTAGCTCTGTTCATTGTCAAAAT	57.201	30.769	0.00	0.00	0.00	1.82
4280	5025	6.278363	TCCAAACCGAATGTAATAGTAGCTC	58.722	40.000	0.00	0.00	0.00	4.09
4281	5026	6.229936	TCCAAACCGAATGTAATAGTAGCT	57.770	37.500	0.00	0.00	0.00	3.32
4282	5027	7.654520	TGTATCCAAACCGAATGTAATAGTAGC	59.345	37.037	0.00	0.00	0.00	3.58
4283	5028	9.537192	TTGTATCCAAACCGAATGTAATAGTAG	57.463	33.333	0.00	0.00	0.00	2.57
4364	5109	8.475331	TCATCCATTAAGTCTTCTTAAACGAC	57.525	34.615	4.86	0.00	45.40	4.34
4385	5130	6.030228	GGGTTGTCGATTCTTTTGATTCATC	58.970	40.000	0.00	0.00	0.00	2.92
4445	5490	2.029964	GTTCGGGTGAGGCGAACA	59.970	61.111	3.17	0.00	40.88	3.18
4528	5576	5.106712	GCAATTATCACTCGTCTGGACAAAA	60.107	40.000	1.63	0.00	0.00	2.44
4553	5601	7.222000	AGATATACTTGTACTAGAGCAAGCC	57.778	40.000	21.77	11.66	44.12	4.35
4604	5653	5.545588	TCAGCTGCTTGATCATACTAATCC	58.454	41.667	9.47	0.00	0.00	3.01
4608	5657	4.813161	GCTTTCAGCTGCTTGATCATACTA	59.187	41.667	9.47	0.00	38.45	1.82
4609	5658	3.626670	GCTTTCAGCTGCTTGATCATACT	59.373	43.478	9.47	0.00	38.45	2.12
4610	5659	3.376234	TGCTTTCAGCTGCTTGATCATAC	59.624	43.478	9.47	0.00	42.97	2.39
4611	5660	3.613030	TGCTTTCAGCTGCTTGATCATA	58.387	40.909	9.47	0.00	42.97	2.15
4612	5661	2.443416	TGCTTTCAGCTGCTTGATCAT	58.557	42.857	9.47	0.00	42.97	2.45
4613	5662	1.900245	TGCTTTCAGCTGCTTGATCA	58.100	45.000	9.47	0.00	42.97	2.92
4614	5663	4.627611	TTATGCTTTCAGCTGCTTGATC	57.372	40.909	9.47	0.00	42.97	2.92
4636	5829	5.308237	AGCTACCTGGCTTGTTATATAGCTT	59.692	40.000	0.00	0.00	40.88	3.74
4641	5834	5.366768	TCTTGAGCTACCTGGCTTGTTATAT	59.633	40.000	0.00	0.00	43.20	0.86
4648	5844	3.777522	AGTTATCTTGAGCTACCTGGCTT	59.222	43.478	0.00	0.00	43.20	4.35
4697	5902	4.154737	TGATCAGTGTTATGAGTTTGCAGC	59.845	41.667	0.00	0.00	31.44	5.25
4793	6005	2.763448	GCTCTAGCTTTTGAGAGGAGGA	59.237	50.000	12.16	0.00	39.74	3.71
4794	6006	3.177997	GCTCTAGCTTTTGAGAGGAGG	57.822	52.381	12.16	0.00	39.74	4.30

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.