AutoCloner

Multiple sequence alignment - TraesCS7A01G107200

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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	TraesCS7A01G107200	chr7A	100.000	4577	0	0	1	4577	64922925	64927501	0.000000e+00	8453.0
1	TraesCS7A01G107200	chr7A	93.355	602	20	3	540	1141	64916904	64917485	0.000000e+00	872.0
2	TraesCS7A01G107200	chr7A	94.096	542	31	1	1	541	678205876	678206417	0.000000e+00	822.0
3	TraesCS7A01G107200	chr7A	94.403	536	24	5	11	541	574152	574686	0.000000e+00	819.0
4	TraesCS7A01G107200	chr7A	93.911	542	27	6	3	542	503243674	503243137	0.000000e+00	813.0
5	TraesCS7A01G107200	chr7B	92.557	3023	158	23	1564	4577	3172632	3175596	0.000000e+00	4274.0
6	TraesCS7A01G107200	chr7B	85.227	616	54	20	733	1324	3170816	3171418	2.360000e-167	599.0
7	TraesCS7A01G107200	chr7D	94.841	2520	98	14	1564	4076	60669673	60672167	0.000000e+00	3904.0
8	TraesCS7A01G107200	chr7D	86.598	679	48	22	685	1324	60667721	60668395	0.000000e+00	710.0
9	TraesCS7A01G107200	chr7D	87.647	340	23	5	4092	4431	60673917	60674237	1.200000e-100	377.0
10	TraesCS7A01G107200	chr7D	87.500	88	3	7	4497	4577	60674213	60674299	1.360000e-15	95.3
11	TraesCS7A01G107200	chr3B	88.010	784	56	12	1564	2336	299127535	299128291	0.000000e+00	893.0
12	TraesCS7A01G107200	chr3B	89.200	500	49	5	2757	3255	299143843	299144338	1.810000e-173	619.0
13	TraesCS7A01G107200	chr3B	87.500	440	39	11	2338	2761	299141058	299141497	1.140000e-135	494.0
14	TraesCS7A01G107200	chr3B	92.012	338	27	0	3252	3589	299144550	299144887	4.140000e-130	475.0
15	TraesCS7A01G107200	chr3B	82.844	443	54	15	865	1296	299120465	299120896	1.200000e-100	377.0
16	TraesCS7A01G107200	chr3A	87.643	785	56	13	1567	2339	264046980	264046225	0.000000e+00	874.0
17	TraesCS7A01G107200	chr3A	93.590	546	30	5	1	543	154727859	154728402	0.000000e+00	809.0
18	TraesCS7A01G107200	chr3A	93.727	542	31	3	2	541	418945317	418945857	0.000000e+00	809.0
19	TraesCS7A01G107200	chr3A	88.755	498	45	10	2757	3253	264025621	264025134	2.360000e-167	599.0
20	TraesCS7A01G107200	chr3A	87.671	438	40	7	2338	2761	264028454	264028017	8.840000e-137	497.0
21	TraesCS7A01G107200	chr3A	92.012	338	27	0	3252	3589	264024931	264024594	4.140000e-130	475.0
22	TraesCS7A01G107200	chr3A	86.236	356	32	5	983	1324	264049031	264048679	2.010000e-98	370.0
23	TraesCS7A01G107200	chr5A	95.396	543	25	0	1	543	229918948	229919490	0.000000e+00	865.0
24	TraesCS7A01G107200	chr5A	94.074	540	31	1	3	542	239586559	239586021	0.000000e+00	819.0
25	TraesCS7A01G107200	chr3D	87.294	787	60	14	1567	2341	225866095	225865337	0.000000e+00	863.0
26	TraesCS7A01G107200	chr3D	90.982	499	41	4	2757	3255	225852769	225852275	0.000000e+00	669.0
27	TraesCS7A01G107200	chr3D	88.182	440	36	8	2338	2761	225855663	225855224	1.140000e-140	510.0
28	TraesCS7A01G107200	chr3D	91.716	338	28	0	3252	3589	225852073	225851736	1.930000e-128	470.0
29	TraesCS7A01G107200	chr3D	83.864	440	37	13	983	1392	225867981	225867546	5.550000e-104	388.0
30	TraesCS7A01G107200	chr2A	94.041	537	31	1	6	541	188012609	188012073	0.000000e+00	813.0
31	TraesCS7A01G107200	chr4A	93.248	548	31	6	3	545	63867937	63868483	0.000000e+00	802.0
32	TraesCS7A01G107200	chr6B	88.400	500	53	5	2757	3255	51909034	51908539	8.480000e-167	597.0
33	TraesCS7A01G107200	chr6B	88.757	338	37	1	3252	3589	51908329	51907993	3.300000e-111	412.0
34	TraesCS7A01G107200	chr2D	81.132	159	28	2	3015	3172	89387859	89388016	4.810000e-25	126.0
35	TraesCS7A01G107200	chr2B	80.120	166	29	4	3010	3172	141988032	141988196	2.240000e-23	121.0

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	TraesCS7A01G107200	chr7A	64922925	64927501	4576	False	8453.000000	8453	100.000000	1	4577	1	chr7A.!!$F3	4576
1	TraesCS7A01G107200	chr7A	64916904	64917485	581	False	872.000000	872	93.355000	540	1141	1	chr7A.!!$F2	601
2	TraesCS7A01G107200	chr7A	678205876	678206417	541	False	822.000000	822	94.096000	1	541	1	chr7A.!!$F4	540
3	TraesCS7A01G107200	chr7A	574152	574686	534	False	819.000000	819	94.403000	11	541	1	chr7A.!!$F1	530
4	TraesCS7A01G107200	chr7A	503243137	503243674	537	True	813.000000	813	93.911000	3	542	1	chr7A.!!$R1	539
5	TraesCS7A01G107200	chr7B	3170816	3175596	4780	False	2436.500000	4274	88.892000	733	4577	2	chr7B.!!$F1	3844
6	TraesCS7A01G107200	chr7D	60667721	60674299	6578	False	1271.575000	3904	89.146500	685	4577	4	chr7D.!!$F1	3892
7	TraesCS7A01G107200	chr3B	299127535	299128291	756	False	893.000000	893	88.010000	1564	2336	1	chr3B.!!$F2	772
8	TraesCS7A01G107200	chr3B	299141058	299144887	3829	False	529.333333	619	89.570667	2338	3589	3	chr3B.!!$F3	1251
9	TraesCS7A01G107200	chr3A	154727859	154728402	543	False	809.000000	809	93.590000	1	543	1	chr3A.!!$F1	542
10	TraesCS7A01G107200	chr3A	418945317	418945857	540	False	809.000000	809	93.727000	2	541	1	chr3A.!!$F2	539
11	TraesCS7A01G107200	chr3A	264046225	264049031	2806	True	622.000000	874	86.939500	983	2339	2	chr3A.!!$R2	1356
12	TraesCS7A01G107200	chr3A	264024594	264028454	3860	True	523.666667	599	89.479333	2338	3589	3	chr3A.!!$R1	1251
13	TraesCS7A01G107200	chr5A	229918948	229919490	542	False	865.000000	865	95.396000	1	543	1	chr5A.!!$F1	542
14	TraesCS7A01G107200	chr5A	239586021	239586559	538	True	819.000000	819	94.074000	3	542	1	chr5A.!!$R1	539
15	TraesCS7A01G107200	chr3D	225865337	225867981	2644	True	625.500000	863	85.579000	983	2341	2	chr3D.!!$R2	1358
16	TraesCS7A01G107200	chr3D	225851736	225855663	3927	True	549.666667	669	90.293333	2338	3589	3	chr3D.!!$R1	1251
17	TraesCS7A01G107200	chr2A	188012073	188012609	536	True	813.000000	813	94.041000	6	541	1	chr2A.!!$R1	535
18	TraesCS7A01G107200	chr4A	63867937	63868483	546	False	802.000000	802	93.248000	3	545	1	chr4A.!!$F1	542
19	TraesCS7A01G107200	chr6B	51907993	51909034	1041	True	504.500000	597	88.578500	2757	3589	2	chr6B.!!$R1	832

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
167	174	0.787084	TGGGCCAAAATGGAAGGGTA	59.213	50.000	2.13	0.00	40.96	3.69	F
424	431	1.063174	GGATGCAAGAGACGAACATGC	59.937	52.381	0.00	0.00	37.52	4.06	F
559	566	1.210204	ACTGGACCACCATCAGCCAT	61.210	55.000	0.00	0.00	45.87	4.40	F
1367	1468	1.576246	CAAATCGACCGTCGTTCTACG	59.424	52.381	19.89	2.75	44.19	3.51	F
2240	4016	2.030805	GCATCCCTTATTGGCGATGTTC	60.031	50.000	0.00	0.00	41.47	3.18	F
3097	7387	3.329520	AGCAACCCTGTTAGATGGTGTTA	59.670	43.478	0.00	0.00	31.32	2.41	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1468	1569	0.111832	TCCGTACACTGTCCACCTCT	59.888	55.000	0.00	0.00	3.69	R
2137	3913	1.243342	TGCGATGCCTTGAAACTGGG	61.243	55.000	0.00	0.00	4.45	R
2301	4077	2.165030	GACCAAAATGATGCTCACTGGG	59.835	50.000	11.77	31.67	4.45	R
3097	7387	2.502538	CCATCCCATGCTTTTCCACAAT	59.497	45.455	0.00	0.00	2.71	R
3483	7991	1.228894	TTCCTCGTCCTGGTGAGCT	60.229	57.895	11.56	0.00	4.09	R
3904	8412	2.552743	CAAGATCATGCATGCCTACAGG	59.447	50.000	22.25	38.53	4.00	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
167	174	0.787084	TGGGCCAAAATGGAAGGGTA	59.213	50.000	2.13	0.00	40.96	3.69
306	313	1.202879	TGGCAAGTTTCGGTCCAATCT	60.203	47.619	0.00	0.00	0.00	2.40
372	379	1.456196	CGGAGGAGATAGAAGCGCCA	61.456	60.000	2.29	0.00	0.00	5.69
424	431	1.063174	GGATGCAAGAGACGAACATGC	59.937	52.381	0.00	0.00	37.52	4.06
433	440	3.940852	AGAGACGAACATGCATGCAAATA	59.059	39.130	26.68	0.00	0.00	1.40
559	566	1.210204	ACTGGACCACCATCAGCCAT	61.210	55.000	0.00	0.00	45.87	4.40
600	607	2.892425	CCGCTGCCGACCTCATTC	60.892	66.667	0.00	0.00	36.29	2.67
675	682	4.103103	CGCGACTGCTGTCCTCGA	62.103	66.667	20.58	0.00	39.94	4.04
684	691	3.758088	CTGTCCTCGATGACCGCCG	62.758	68.421	16.81	1.38	38.37	6.46
1111	1170	2.791655	TCTTCCACGAGCAGAGTAAGA	58.208	47.619	0.00	0.00	0.00	2.10
1231	1311	2.354103	CCCAAAAGAGTGAGCAGATCGA	60.354	50.000	0.00	0.00	0.00	3.59
1234	1314	4.240888	CAAAAGAGTGAGCAGATCGAGAA	58.759	43.478	0.00	0.00	0.00	2.87
1241	1321	1.593750	GCAGATCGAGAATGCCGCT	60.594	57.895	7.80	0.00	33.81	5.52
1283	1363	5.584649	CAGGAAATATCACGGTTATGTGTGT	59.415	40.000	0.00	0.00	40.74	3.72
1306	1392	2.034124	CATTAGATTGGGGCTGGGTTG	58.966	52.381	0.00	0.00	0.00	3.77
1313	1399	1.984026	GGGGCTGGGTTGTCCATTG	60.984	63.158	0.00	0.00	46.01	2.82
1324	1410	4.331968	GGTTGTCCATTGTTAGGTCATCA	58.668	43.478	0.00	0.00	0.00	3.07
1325	1411	4.764823	GGTTGTCCATTGTTAGGTCATCAA	59.235	41.667	0.00	0.00	0.00	2.57
1327	1413	4.588899	TGTCCATTGTTAGGTCATCAAGG	58.411	43.478	0.00	0.00	0.00	3.61
1334	1435	3.072330	TGTTAGGTCATCAAGGTCTTGCA	59.928	43.478	5.88	0.00	40.24	4.08
1335	1436	2.191128	AGGTCATCAAGGTCTTGCAC	57.809	50.000	5.88	3.19	40.24	4.57
1360	1461	1.915350	TCGAATTCAAATCGACCGTCG	59.085	47.619	14.94	14.94	43.76	5.12
1363	1464	3.656618	GAATTCAAATCGACCGTCGTTC	58.343	45.455	19.89	10.84	41.35	3.95
1364	1465	2.427232	TTCAAATCGACCGTCGTTCT	57.573	45.000	19.89	4.46	41.35	3.01
1365	1466	3.557577	TTCAAATCGACCGTCGTTCTA	57.442	42.857	19.89	1.61	41.35	2.10
1366	1467	2.855180	TCAAATCGACCGTCGTTCTAC	58.145	47.619	19.89	0.00	41.35	2.59
1367	1468	1.576246	CAAATCGACCGTCGTTCTACG	59.424	52.381	19.89	2.75	44.19	3.51
1420	1521	9.880157	ATATAGTGTTGGTTATTTACTGACGTT	57.120	29.630	0.00	0.00	0.00	3.99
1423	1524	5.842327	GTGTTGGTTATTTACTGACGTTTCG	59.158	40.000	0.00	0.00	0.00	3.46
1424	1525	5.050227	TGTTGGTTATTTACTGACGTTTCGG	60.050	40.000	0.00	0.00	0.00	4.30
1425	1526	4.880759	TGGTTATTTACTGACGTTTCGGA	58.119	39.130	0.00	0.00	31.76	4.55
1426	1527	5.295950	TGGTTATTTACTGACGTTTCGGAA	58.704	37.500	0.00	0.00	31.76	4.30
1427	1528	5.933463	TGGTTATTTACTGACGTTTCGGAAT	59.067	36.000	0.00	0.00	31.76	3.01
1429	1530	7.276218	TGGTTATTTACTGACGTTTCGGAATAG	59.724	37.037	0.00	0.00	31.76	1.73
1430	1531	7.276438	GGTTATTTACTGACGTTTCGGAATAGT	59.724	37.037	0.00	0.00	31.76	2.12
1440	1541	7.814107	TGACGTTTCGGAATAGTTAGTTAACAT	59.186	33.333	8.61	0.00	38.62	2.71
1484	1585	4.803098	AATACAGAGGTGGACAGTGTAC	57.197	45.455	0.00	0.00	0.00	2.90
1494	1599	2.494471	TGGACAGTGTACGGATTGTAGG	59.506	50.000	0.00	0.00	32.51	3.18
1526	1631	3.369576	GGTAGAACTTGCCTCTTACCCAG	60.370	52.174	0.00	0.00	0.00	4.45
1528	1633	2.711547	AGAACTTGCCTCTTACCCAGTT	59.288	45.455	0.00	0.00	0.00	3.16
1529	1634	3.908103	AGAACTTGCCTCTTACCCAGTTA	59.092	43.478	0.00	0.00	0.00	2.24
1565	3317	7.880160	ATTGCATATTAACTGAACTTGCCTA	57.120	32.000	0.00	0.00	30.60	3.93
1597	3349	4.816385	TGCACATTTCTTCCTAATCGATCC	59.184	41.667	0.00	0.00	0.00	3.36
1642	3394	4.098654	TGTTGTGTTCACCCCTTATTTGTG	59.901	41.667	0.37	0.00	0.00	3.33
1675	3432	5.858159	TGTTATTTTTGTCGTTTTCTGCG	57.142	34.783	0.00	0.00	0.00	5.18
1677	3434	2.923605	TTTTTGTCGTTTTCTGCGGT	57.076	40.000	0.00	0.00	0.00	5.68
1687	3444	3.906008	CGTTTTCTGCGGTATTGTTTCTG	59.094	43.478	0.00	0.00	0.00	3.02
1890	3656	7.239763	TGTCACACTCTGTAGATGGATAAAA	57.760	36.000	0.00	0.00	0.00	1.52
1972	3747	6.155910	AGTGGTAGATGACACTTTCTGATCAT	59.844	38.462	0.00	0.00	45.03	2.45
1973	3748	6.820656	GTGGTAGATGACACTTTCTGATCATT	59.179	38.462	0.00	0.00	31.96	2.57
2017	3792	4.808077	CAGGATGCTGCTTATGTTGTAG	57.192	45.455	0.00	0.00	0.00	2.74
2018	3793	4.194640	CAGGATGCTGCTTATGTTGTAGT	58.805	43.478	0.00	0.00	0.00	2.73
2019	3794	4.034858	CAGGATGCTGCTTATGTTGTAGTG	59.965	45.833	0.00	0.00	0.00	2.74
2020	3795	3.941483	GGATGCTGCTTATGTTGTAGTGT	59.059	43.478	0.00	0.00	0.00	3.55
2021	3796	4.396166	GGATGCTGCTTATGTTGTAGTGTT	59.604	41.667	0.00	0.00	0.00	3.32
2022	3797	4.747540	TGCTGCTTATGTTGTAGTGTTG	57.252	40.909	0.00	0.00	0.00	3.33
2023	3798	4.133820	TGCTGCTTATGTTGTAGTGTTGT	58.866	39.130	0.00	0.00	0.00	3.32
2024	3799	5.301555	TGCTGCTTATGTTGTAGTGTTGTA	58.698	37.500	0.00	0.00	0.00	2.41
2047	3822	9.559732	TGTACACTGCATCTAATTATTATTGCT	57.440	29.630	15.88	4.41	0.00	3.91
2240	4016	2.030805	GCATCCCTTATTGGCGATGTTC	60.031	50.000	0.00	0.00	41.47	3.18
2301	4077	6.858478	GTCTTAAGAGGTTTGTGCTCAATTTC	59.142	38.462	5.12	1.44	33.32	2.17
2531	4307	9.218440	CTTGTTTTAACCATTGCTTTATTCCAT	57.782	29.630	0.00	0.00	0.00	3.41
2560	4336	7.643764	CCTCGCGATGTTTAATTGTTCATTATT	59.356	33.333	10.36	0.00	0.00	1.40
2938	7227	5.820947	TCTGACACTAAACCTGTTTTCTTCC	59.179	40.000	0.00	0.00	34.23	3.46
3097	7387	3.329520	AGCAACCCTGTTAGATGGTGTTA	59.670	43.478	0.00	0.00	31.32	2.41
3188	7478	3.821033	GAGGTTGTGCTTTACTTCACCAT	59.179	43.478	0.00	0.00	32.51	3.55
3225	7515	7.718334	TCTTATTTAGGTCATCTCAGACACA	57.282	36.000	0.00	0.00	40.29	3.72
3483	7991	3.625764	AGAAAGTGTTGCGCAAGAAAGTA	59.374	39.130	25.78	0.00	33.67	2.24
3502	8010	1.216710	GCTCACCAGGACGAGGAAG	59.783	63.158	11.28	0.00	0.00	3.46
3530	8038	0.898320	ATGCTTAGTGGCACTCGAGT	59.102	50.000	25.80	13.58	45.36	4.18
3639	8147	6.071952	GCCTTCACCATCTTCAGTTTGAATTA	60.072	38.462	0.00	0.00	35.59	1.40
3709	8217	4.349663	TTCAATAATTTTGGGTCGAGCG	57.650	40.909	8.77	0.00	0.00	5.03
3823	8331	1.225745	GCGTTCACTGCGTGCATAC	60.226	57.895	0.00	0.00	32.98	2.39
3824	8332	1.626654	GCGTTCACTGCGTGCATACT	61.627	55.000	0.00	0.00	32.98	2.12
3892	8400	1.686052	GTGAGGGGAAAACAACATGCA	59.314	47.619	0.00	0.00	0.00	3.96
3904	8412	2.816087	ACAACATGCATCTTGAGGTGTC	59.184	45.455	19.92	0.00	0.00	3.67
3994	8502	8.429641	TCCAGATTTATTAGTCCCACTTGTATC	58.570	37.037	0.00	0.00	0.00	2.24
4176	10434	2.356330	CCTGGACGGAGAGAGTAGAAGT	60.356	54.545	0.00	0.00	33.16	3.01
4238	10496	6.256757	ACTTTCATAGTCGCTAGATTTTCAGC	59.743	38.462	0.00	0.00	28.23	4.26
4242	10500	6.763135	TCATAGTCGCTAGATTTTCAGCAATT	59.237	34.615	0.00	0.00	37.66	2.32
4310	10568	3.945285	ACTGCCATACATTTTACCGGAAG	59.055	43.478	9.46	0.00	0.00	3.46
4326	10584	8.716674	TTACCGGAAGTATATTCCTACATCTT	57.283	34.615	9.46	0.00	36.45	2.40
4361	10619	6.916360	TTATTGAATTTTCTTGCTCTGGGT	57.084	33.333	0.00	0.00	0.00	4.51
4413	10671	1.995376	AGCCCCGTCAAATTTTGAGT	58.005	45.000	12.02	0.00	41.01	3.41
4415	10673	1.339929	GCCCCGTCAAATTTTGAGTGT	59.660	47.619	12.02	0.00	41.01	3.55
4416	10674	2.607038	GCCCCGTCAAATTTTGAGTGTC	60.607	50.000	12.02	0.35	41.01	3.67
4423	10681	5.435557	GTCAAATTTTGAGTGTCGAGAGTG	58.564	41.667	12.02	0.00	41.01	3.51
4425	10683	6.200286	GTCAAATTTTGAGTGTCGAGAGTGTA	59.800	38.462	12.02	0.00	41.01	2.90
4428	10686	7.813852	AATTTTGAGTGTCGAGAGTGTATAC	57.186	36.000	0.00	0.00	0.00	1.47
4456	10714	9.932207	TGGATTCGTATTTGAAAGTAGTTCTTA	57.068	29.630	0.00	0.00	37.13	2.10
4531	10789	8.749354	AGGTGAACTTTGACTCAAAATTTAAGT	58.251	29.630	5.72	5.98	32.75	2.24
4535	10793	6.816136	ACTTTGACTCAAAATTTAAGTGGGG	58.184	36.000	10.07	2.74	32.75	4.96

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
21	23	0.179056	GATCCCCTCCGAAATTCGCA	60.179	55.000	10.24	0.00	38.82	5.10
167	174	0.319083	CATGTGTGTTGCAGCCCAAT	59.681	50.000	0.00	0.00	35.55	3.16
306	313	2.966516	GTGTGGGGGTTAAACATTTCCA	59.033	45.455	0.00	0.00	0.00	3.53
372	379	1.001815	CCGTTGTCCGTTTTGCATTCT	60.002	47.619	0.00	0.00	33.66	2.40
433	440	7.685641	TGCATATCATGTCATCATGTGCATTTT	60.686	33.333	15.47	0.10	46.51	1.82
619	626	3.777925	CAGCCAACTTCCGCGACG	61.778	66.667	8.23	0.00	0.00	5.12
675	682	4.910585	GATTCGGCCGGCGGTCAT	62.911	66.667	31.67	23.19	0.00	3.06
1111	1170	2.423538	GCGAGGGAATGTGTTTATGCTT	59.576	45.455	0.00	0.00	0.00	3.91
1192	1272	3.119096	GCCGCCCGAGAAGAACAC	61.119	66.667	0.00	0.00	0.00	3.32
1231	1311	1.141053	CCTAACCCTAAGCGGCATTCT	59.859	52.381	1.45	0.00	0.00	2.40
1234	1314	0.693092	TCCCTAACCCTAAGCGGCAT	60.693	55.000	1.45	0.00	0.00	4.40
1241	1321	2.181975	CTGAACCGTCCCTAACCCTAA	58.818	52.381	0.00	0.00	0.00	2.69
1306	1392	4.589908	ACCTTGATGACCTAACAATGGAC	58.410	43.478	0.00	0.00	0.00	4.02
1313	1399	3.437049	GTGCAAGACCTTGATGACCTAAC	59.563	47.826	13.44	0.00	42.93	2.34
1324	1410	2.839486	TCGAATCTGTGCAAGACCTT	57.161	45.000	0.00	0.00	37.88	3.50
1325	1411	2.839486	TTCGAATCTGTGCAAGACCT	57.161	45.000	0.00	0.00	37.88	3.85
1327	1413	4.668576	TGAATTCGAATCTGTGCAAGAC	57.331	40.909	11.83	0.00	37.88	3.01
1334	1435	4.032900	CGGTCGATTTGAATTCGAATCTGT	59.967	41.667	31.80	11.60	42.10	3.41
1335	1436	4.032900	ACGGTCGATTTGAATTCGAATCTG	59.967	41.667	31.80	26.45	42.10	2.90
1359	1460	2.848887	CTGAGCAACTCATCGTAGAACG	59.151	50.000	0.00	0.00	43.58	3.95
1360	1461	3.839293	ACTGAGCAACTCATCGTAGAAC	58.161	45.455	0.00	0.00	43.58	3.01
1363	1464	3.838120	TGAACTGAGCAACTCATCGTAG	58.162	45.455	0.00	0.00	39.92	3.51
1364	1465	3.934457	TGAACTGAGCAACTCATCGTA	57.066	42.857	0.00	0.00	39.92	3.43
1365	1466	2.820059	TGAACTGAGCAACTCATCGT	57.180	45.000	0.00	0.00	39.92	3.73
1366	1467	4.675190	AAATGAACTGAGCAACTCATCG	57.325	40.909	0.00	0.00	39.92	3.84
1367	1468	5.628193	CACAAAATGAACTGAGCAACTCATC	59.372	40.000	0.00	0.00	39.92	2.92
1368	1469	5.300034	TCACAAAATGAACTGAGCAACTCAT	59.700	36.000	0.00	0.00	35.54	2.90
1369	1470	4.639755	TCACAAAATGAACTGAGCAACTCA	59.360	37.500	0.00	0.00	34.36	3.41
1402	1503	5.295950	TCCGAAACGTCAGTAAATAACCAA	58.704	37.500	0.00	0.00	0.00	3.67
1405	1506	8.177980	ACTATTCCGAAACGTCAGTAAATAAC	57.822	34.615	0.00	0.00	0.00	1.89
1458	1559	5.995897	ACACTGTCCACCTCTGTATTTTTAC	59.004	40.000	0.00	0.00	0.00	2.01
1464	1565	2.753452	CGTACACTGTCCACCTCTGTAT	59.247	50.000	0.00	0.00	0.00	2.29
1467	1568	0.243907	CCGTACACTGTCCACCTCTG	59.756	60.000	0.00	0.00	0.00	3.35
1468	1569	0.111832	TCCGTACACTGTCCACCTCT	59.888	55.000	0.00	0.00	0.00	3.69
1484	1585	3.262420	CCAAAGAGTGACCTACAATCCG	58.738	50.000	0.00	0.00	43.50	4.18
1494	1599	3.498777	GGCAAGTTCTACCAAAGAGTGAC	59.501	47.826	0.00	0.00	35.05	3.67
1558	1663	2.557924	TGTGCAGAACCAAATAGGCAAG	59.442	45.455	0.00	0.00	43.14	4.01
1559	1664	2.591923	TGTGCAGAACCAAATAGGCAA	58.408	42.857	0.00	0.00	43.14	4.52
1561	1666	3.874392	AATGTGCAGAACCAAATAGGC	57.126	42.857	0.00	0.00	43.14	3.93
1565	3317	4.590222	AGGAAGAAATGTGCAGAACCAAAT	59.410	37.500	0.00	0.00	0.00	2.32
1597	3349	5.713389	ACATATGCACATCCAAGGATAATGG	59.287	40.000	1.58	0.00	39.41	3.16
1642	3394	9.988350	AACGACAAAAATAACATCATCAGATAC	57.012	29.630	0.00	0.00	31.88	2.24
1687	3444	7.172703	ACGGGATTGCTAAGCTTACAAATATAC	59.827	37.037	18.78	8.81	0.00	1.47
1705	3462	4.433186	TCAAAATGCTAACACGGGATTG	57.567	40.909	0.00	0.00	0.00	2.67
1799	3562	8.756927	AGTGATCAAAGAAGATAGAGTCAATCA	58.243	33.333	0.00	0.00	0.00	2.57
1803	3566	9.249053	ACTAAGTGATCAAAGAAGATAGAGTCA	57.751	33.333	0.00	0.00	0.00	3.41
1804	3567	9.730420	GACTAAGTGATCAAAGAAGATAGAGTC	57.270	37.037	0.00	0.00	0.00	3.36
1805	3568	8.691797	GGACTAAGTGATCAAAGAAGATAGAGT	58.308	37.037	0.00	0.00	0.00	3.24
1828	3594	2.996249	TCATGAGCTTGATCAGGGAC	57.004	50.000	6.99	0.00	32.00	4.46
1890	3656	9.520515	AAGAAAAACTTACAGATGGATACACAT	57.479	29.630	0.00	0.00	43.74	3.21
1972	3747	5.063944	GCAGATAAGCGTTCAGAAGATCAAA	59.936	40.000	0.00	0.00	0.00	2.69
1973	3748	4.568359	GCAGATAAGCGTTCAGAAGATCAA	59.432	41.667	0.00	0.00	0.00	2.57
1984	3759	1.303309	GCATCCTGCAGATAAGCGTT	58.697	50.000	17.39	0.00	44.26	4.84
2021	3796	9.559732	AGCAATAATAATTAGATGCAGTGTACA	57.440	29.630	13.58	0.00	35.53	2.90
2067	3842	7.329226	GCTCACAACAGCACAAACAATTATAAT	59.671	33.333	0.00	0.00	39.43	1.28
2137	3913	1.243342	TGCGATGCCTTGAAACTGGG	61.243	55.000	0.00	0.00	0.00	4.45
2240	4016	2.930950	TGAAGACCCTTGTCCAACTTG	58.069	47.619	0.00	0.00	42.81	3.16
2301	4077	2.165030	GACCAAAATGATGCTCACTGGG	59.835	50.000	11.77	0.00	31.67	4.45
2324	4100	6.236017	TCAAGTACGTTGATTTAGCAAAGG	57.764	37.500	0.00	0.00	40.45	3.11
2518	4294	2.878406	GCGAGGCTATGGAATAAAGCAA	59.122	45.455	0.00	0.00	38.01	3.91
2531	4307	3.527533	ACAATTAAACATCGCGAGGCTA	58.472	40.909	22.18	9.90	0.00	3.93
2596	4372	6.490721	AGAAGTAGTACCCCGATAAAGATCAG	59.509	42.308	0.00	0.00	31.78	2.90
2922	7209	6.843752	TCCTACATGGAAGAAAACAGGTTTA	58.156	36.000	0.00	0.00	42.94	2.01
2938	7227	3.868757	TGAGAACGAAGGTCCTACATG	57.131	47.619	0.00	0.00	0.00	3.21
3097	7387	2.502538	CCATCCCATGCTTTTCCACAAT	59.497	45.455	0.00	0.00	0.00	2.71
3483	7991	1.228894	TTCCTCGTCCTGGTGAGCT	60.229	57.895	11.56	0.00	0.00	4.09
3502	8010	1.599542	GCCACTAAGCATGGAATCGTC	59.400	52.381	0.00	0.00	39.87	4.20
3546	8054	3.775654	GTAGAGCTGGGTGGCGCT	61.776	66.667	7.64	0.00	44.02	5.92
3644	8152	6.376864	ACTCACTGCGCAGATAGAGATATAAT	59.623	38.462	38.93	25.21	33.31	1.28
3645	8153	5.707764	ACTCACTGCGCAGATAGAGATATAA	59.292	40.000	38.93	18.18	33.31	0.98
3684	8192	6.237542	CGCTCGACCCAAAATTATTGAAATTG	60.238	38.462	0.00	0.00	0.00	2.32
3685	8193	5.804979	CGCTCGACCCAAAATTATTGAAATT	59.195	36.000	0.00	0.00	0.00	1.82
3709	8217	6.109359	ACTACATGGTCAGCTTTAGAACATC	58.891	40.000	0.22	0.00	41.27	3.06
3753	8261	7.776030	TCTGTTTGTTCCATAGGTCTTAAAACA	59.224	33.333	0.00	0.00	34.75	2.83
3763	8271	5.982890	AATGGTTCTGTTTGTTCCATAGG	57.017	39.130	0.00	0.00	37.84	2.57
3823	8331	6.205464	TCTCACAATTTCAGCCAGAGTAAAAG	59.795	38.462	0.00	0.00	0.00	2.27
3824	8332	6.061441	TCTCACAATTTCAGCCAGAGTAAAA	58.939	36.000	0.00	0.00	0.00	1.52
3892	8400	1.834263	GCCTACAGGACACCTCAAGAT	59.166	52.381	0.00	0.00	37.39	2.40
3904	8412	2.552743	CAAGATCATGCATGCCTACAGG	59.447	50.000	22.25	0.00	38.53	4.00
3971	8479	9.838339	CAAGATACAAGTGGGACTAATAAATCT	57.162	33.333	0.00	0.00	0.00	2.40
3986	8494	8.682936	ATCAAAGTTTCACTCAAGATACAAGT	57.317	30.769	0.00	0.00	0.00	3.16
3994	8502	9.450807	AAATTTACGATCAAAGTTTCACTCAAG	57.549	29.630	0.00	0.00	0.00	3.02
4176	10434	9.836864	AGACTGAACTCAATATACATGCAATTA	57.163	29.630	0.00	0.00	0.00	1.40
4221	10479	5.886960	AAATTGCTGAAAATCTAGCGACT	57.113	34.783	0.00	0.00	42.74	4.18
4280	10538	5.528043	AAAATGTATGGCAGTGTTCAACA	57.472	34.783	0.00	0.00	0.00	3.33
4281	10539	5.861787	GGTAAAATGTATGGCAGTGTTCAAC	59.138	40.000	0.00	0.00	0.00	3.18
4283	10541	4.155099	CGGTAAAATGTATGGCAGTGTTCA	59.845	41.667	0.00	0.00	0.00	3.18
4310	10568	6.331061	CACCGCCTAAGATGTAGGAATATAC	58.669	44.000	3.53	0.00	36.85	1.47
4326	10584	3.655615	ATTCAATAAACCCACCGCCTA	57.344	42.857	0.00	0.00	0.00	3.93
4361	10619	4.382685	GGACGAAGAATTCCACATCTACCA	60.383	45.833	0.65	0.00	43.81	3.25
4413	10671	5.220796	CGAATCCAAGTATACACTCTCGACA	60.221	44.000	5.50	0.00	32.29	4.35
4415	10673	4.880120	ACGAATCCAAGTATACACTCTCGA	59.120	41.667	5.50	0.00	32.29	4.04
4416	10674	5.171147	ACGAATCCAAGTATACACTCTCG	57.829	43.478	5.50	7.87	32.29	4.04
4425	10683	9.886132	ACTACTTTCAAATACGAATCCAAGTAT	57.114	29.630	0.00	0.00	35.29	2.12
4428	10686	8.936864	AGAACTACTTTCAAATACGAATCCAAG	58.063	33.333	0.00	0.00	36.57	3.61
4535	10793	7.215719	ACTTTCTCTGTTTGGGTTTATAAGC	57.784	36.000	0.00	0.00	0.00	3.09

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.