AutoCloner

Multiple sequence alignment - TraesCS7D01G071700

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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	TraesCS7D01G071700	chr7D	100.000	2405	0	0	1	2405	42197537	42195133	0.000000e+00	4442.0
1	TraesCS7D01G071700	chr3A	90.212	1890	118	30	138	1972	15429087	15430964	0.000000e+00	2403.0
2	TraesCS7D01G071700	chr3A	89.885	1394	86	14	224	1577	12177445	12176067	0.000000e+00	1742.0
3	TraesCS7D01G071700	chr3A	94.286	420	23	1	1987	2405	12175371	12174952	2.020000e-180	641.0
4	TraesCS7D01G071700	chr3A	92.890	436	28	3	1972	2405	15430990	15431424	4.360000e-177	630.0
5	TraesCS7D01G071700	chr3A	91.453	117	10	0	1856	1972	12175864	12175748	6.880000e-36	161.0
6	TraesCS7D01G071700	chr3A	92.473	93	6	1	138	229	12179025	12178933	5.390000e-27	132.0
7	TraesCS7D01G071700	chr3A	88.679	53	6	0	568	620	38621385	38621437	5.550000e-07	65.8
8	TraesCS7D01G071700	chr3B	91.009	1735	92	17	138	1818	11924166	11925890	0.000000e+00	2281.0
9	TraesCS7D01G071700	chr3B	90.444	450	26	8	1972	2405	11927460	11927908	5.770000e-161	577.0
10	TraesCS7D01G071700	chr3B	96.703	273	9	0	1700	1972	11959419	11959147	2.820000e-124	455.0
11	TraesCS7D01G071700	chr3B	95.902	244	8	2	1972	2213	11959121	11958878	6.230000e-106	394.0
12	TraesCS7D01G071700	chr3B	94.017	117	6	1	9	125	327814731	327814616	2.460000e-40	176.0
13	TraesCS7D01G071700	chr3B	96.970	66	1	1	1551	1615	11925585	11925650	2.530000e-20	110.0
14	TraesCS7D01G071700	chrUn	88.978	1751	112	26	138	1815	36300405	36298663	0.000000e+00	2089.0
15	TraesCS7D01G071700	chrUn	91.954	435	34	1	1972	2405	35514435	35514869	2.040000e-170	608.0
16	TraesCS7D01G071700	chrUn	92.558	430	17	5	495	912	476365714	476365288	9.510000e-169	603.0
17	TraesCS7D01G071700	chrUn	90.889	450	24	8	1972	2405	36296978	36296530	2.660000e-164	588.0
18	TraesCS7D01G071700	chrUn	94.167	360	21	0	2046	2405	32300198	32299839	1.260000e-152	549.0
19	TraesCS7D01G071700	chrUn	87.557	442	34	8	1551	1972	35513969	35514409	2.150000e-135	492.0
20	TraesCS7D01G071700	chrUn	90.884	362	32	1	1177	1537	35513625	35513986	3.590000e-133	484.0
21	TraesCS7D01G071700	chrUn	95.238	273	13	0	1700	1972	36476640	36476912	1.320000e-117	433.0
22	TraesCS7D01G071700	chrUn	95.902	244	8	2	1972	2213	36476938	36477181	6.230000e-106	394.0
23	TraesCS7D01G071700	chrUn	94.175	206	12	0	2200	2405	267482407	267482612	4.990000e-82	315.0
24	TraesCS7D01G071700	chrUn	92.857	140	10	0	138	277	36318091	36318230	1.130000e-48	204.0
25	TraesCS7D01G071700	chrUn	96.970	66	1	1	1551	1615	36298967	36298902	2.530000e-20	110.0
26	TraesCS7D01G071700	chr3D	87.613	1881	123	42	138	1972	5815896	5814080	0.000000e+00	2082.0
27	TraesCS7D01G071700	chr3D	94.266	436	23	2	1972	2405	5814054	5813619	0.000000e+00	665.0
28	TraesCS7D01G071700	chr3D	88.679	53	6	0	568	620	29308931	29308879	5.550000e-07	65.8
29	TraesCS7D01G071700	chr7B	79.667	600	96	11	839	1412	28686846	28687445	2.230000e-110	409.0
30	TraesCS7D01G071700	chr4D	78.125	544	104	13	999	1532	298770564	298770026	4.960000e-87	331.0
31	TraesCS7D01G071700	chr1D	79.433	423	78	8	999	1417	290978548	290978965	8.410000e-75	291.0
32	TraesCS7D01G071700	chr7A	94.783	115	5	1	11	125	595642597	595642484	6.830000e-41	178.0
33	TraesCS7D01G071700	chr2B	92.683	123	7	2	4	125	358331847	358331726	2.460000e-40	176.0
34	TraesCS7D01G071700	chr2B	90.476	126	11	1	1	125	678568617	678568742	5.320000e-37	165.0
35	TraesCS7D01G071700	chr2D	93.966	116	6	1	11	126	440320452	440320338	8.840000e-40	174.0
36	TraesCS7D01G071700	chr6B	91.935	124	7	3	4	125	113707127	113707249	1.140000e-38	171.0
37	TraesCS7D01G071700	chr5B	91.935	124	7	3	4	125	116585507	116585385	1.140000e-38	171.0
38	TraesCS7D01G071700	chr6D	92.373	118	7	2	8	125	22072645	22072530	1.480000e-37	167.0
39	TraesCS7D01G071700	chr4B	91.129	124	8	3	4	125	666894969	666895091	5.320000e-37	165.0

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	TraesCS7D01G071700	chr7D	42195133	42197537	2404	True	4442.000000	4442	100.000000	1	2405	1	chr7D.!!$R1	2404
1	TraesCS7D01G071700	chr3A	15429087	15431424	2337	False	1516.500000	2403	91.551000	138	2405	2	chr3A.!!$F2	2267
2	TraesCS7D01G071700	chr3A	12174952	12179025	4073	True	669.000000	1742	92.024250	138	2405	4	chr3A.!!$R1	2267
3	TraesCS7D01G071700	chr3B	11924166	11927908	3742	False	989.333333	2281	92.807667	138	2405	3	chr3B.!!$F1	2267
4	TraesCS7D01G071700	chr3B	11958878	11959419	541	True	424.500000	455	96.302500	1700	2213	2	chr3B.!!$R2	513
5	TraesCS7D01G071700	chrUn	36296530	36300405	3875	True	929.000000	2089	92.279000	138	2405	3	chrUn.!!$R3	2267
6	TraesCS7D01G071700	chrUn	35513625	35514869	1244	False	528.000000	608	90.131667	1177	2405	3	chrUn.!!$F3	1228
7	TraesCS7D01G071700	chrUn	36476640	36477181	541	False	413.500000	433	95.570000	1700	2213	2	chrUn.!!$F4	513
8	TraesCS7D01G071700	chr3D	5813619	5815896	2277	True	1373.500000	2082	90.939500	138	2405	2	chr3D.!!$R2	2267
9	TraesCS7D01G071700	chr7B	28686846	28687445	599	False	409.000000	409	79.667000	839	1412	1	chr7B.!!$F1	573
10	TraesCS7D01G071700	chr4D	298770026	298770564	538	True	331.000000	331	78.125000	999	1532	1	chr4D.!!$R1	533

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	End Stability	Orientation
126	127	0.034863	AGACAACCAAACACCACCGT	60.035	50.0	4.83	F
451	1988	0.036010	ATGTCCCGGTGAAGCAAGAG	60.036	55.0	2.85	F
928	2492	0.387929	AAGCTCGACGACCACAAGAA	59.612	50.0	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1255	2848	0.246635	CTCGTCACCTGGATTTCCGT	59.753	55.000	39.43	4.69	R
1364	2957	1.078426	CGAACATGGAGGGACACCC	60.078	63.158	45.90	4.61	R
2317	5978	1.136252	CACCTTCGTCTTGCATCGTTG	60.136	52.381	0.00	4.10	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
52	53	9.880064	CTTTTTACTAAAAGTCCTTAGAAGCAC	57.120	33.333	0.00	0.00	43.34	4.40
53	54	7.974482	TTTACTAAAAGTCCTTAGAAGCACC	57.026	36.000	0.00	0.00	33.78	5.01
54	55	5.827326	ACTAAAAGTCCTTAGAAGCACCT	57.173	39.130	0.00	0.00	33.78	4.00
55	56	6.189036	ACTAAAAGTCCTTAGAAGCACCTT	57.811	37.500	0.00	0.00	33.78	3.50
56	57	6.602278	ACTAAAAGTCCTTAGAAGCACCTTT	58.398	36.000	0.00	0.00	33.78	3.11
57	58	7.061054	ACTAAAAGTCCTTAGAAGCACCTTTT	58.939	34.615	12.39	12.39	33.78	2.27
58	59	6.791867	AAAAGTCCTTAGAAGCACCTTTTT	57.208	33.333	0.00	0.00	29.48	1.94
59	60	5.774498	AAGTCCTTAGAAGCACCTTTTTG	57.226	39.130	0.00	0.00	0.00	2.44
60	61	5.048846	AGTCCTTAGAAGCACCTTTTTGA	57.951	39.130	0.00	0.00	0.00	2.69
61	62	5.066593	AGTCCTTAGAAGCACCTTTTTGAG	58.933	41.667	0.00	0.00	0.00	3.02
62	63	5.063880	GTCCTTAGAAGCACCTTTTTGAGA	58.936	41.667	0.00	0.00	0.00	3.27
63	64	5.180304	GTCCTTAGAAGCACCTTTTTGAGAG	59.820	44.000	0.00	0.00	0.00	3.20
64	65	5.066593	CCTTAGAAGCACCTTTTTGAGAGT	58.933	41.667	0.00	0.00	0.00	3.24
65	66	5.180304	CCTTAGAAGCACCTTTTTGAGAGTC	59.820	44.000	0.00	0.00	0.00	3.36
66	67	4.429854	AGAAGCACCTTTTTGAGAGTCT	57.570	40.909	0.00	0.00	0.00	3.24
67	68	4.786425	AGAAGCACCTTTTTGAGAGTCTT	58.214	39.130	0.00	0.00	0.00	3.01
68	69	5.196695	AGAAGCACCTTTTTGAGAGTCTTT	58.803	37.500	0.00	0.00	0.00	2.52
69	70	5.654209	AGAAGCACCTTTTTGAGAGTCTTTT	59.346	36.000	0.00	0.00	0.00	2.27
70	71	5.921962	AGCACCTTTTTGAGAGTCTTTTT	57.078	34.783	0.00	0.00	0.00	1.94
71	72	5.654497	AGCACCTTTTTGAGAGTCTTTTTG	58.346	37.500	0.00	0.00	0.00	2.44
72	73	5.418840	AGCACCTTTTTGAGAGTCTTTTTGA	59.581	36.000	0.00	0.00	0.00	2.69
73	74	6.071391	AGCACCTTTTTGAGAGTCTTTTTGAA	60.071	34.615	0.00	0.00	0.00	2.69
74	75	6.589907	GCACCTTTTTGAGAGTCTTTTTGAAA	59.410	34.615	0.00	0.00	0.00	2.69
75	76	7.117667	GCACCTTTTTGAGAGTCTTTTTGAAAA	59.882	33.333	0.00	0.00	0.00	2.29
76	77	8.987890	CACCTTTTTGAGAGTCTTTTTGAAAAA	58.012	29.630	2.83	2.83	0.00	1.94
118	119	4.818642	GTCCTAGGACTAGACAACCAAAC	58.181	47.826	31.12	3.26	41.57	2.93
119	120	4.282703	GTCCTAGGACTAGACAACCAAACA	59.717	45.833	31.12	0.00	41.57	2.83
120	121	4.282703	TCCTAGGACTAGACAACCAAACAC	59.717	45.833	7.62	0.00	35.21	3.32
121	122	3.487120	AGGACTAGACAACCAAACACC	57.513	47.619	0.00	0.00	0.00	4.16
122	123	2.775384	AGGACTAGACAACCAAACACCA	59.225	45.455	0.00	0.00	0.00	4.17
123	124	2.876550	GGACTAGACAACCAAACACCAC	59.123	50.000	0.00	0.00	0.00	4.16
124	125	2.876550	GACTAGACAACCAAACACCACC	59.123	50.000	0.00	0.00	0.00	4.61
125	126	1.871039	CTAGACAACCAAACACCACCG	59.129	52.381	0.00	0.00	0.00	4.94
126	127	0.034863	AGACAACCAAACACCACCGT	60.035	50.000	0.00	0.00	0.00	4.83
127	128	0.379316	GACAACCAAACACCACCGTC	59.621	55.000	0.00	0.00	0.00	4.79
128	129	0.034863	ACAACCAAACACCACCGTCT	60.035	50.000	0.00	0.00	0.00	4.18
129	130	0.380378	CAACCAAACACCACCGTCTG	59.620	55.000	0.00	0.00	0.00	3.51
130	131	0.253610	AACCAAACACCACCGTCTGA	59.746	50.000	0.00	0.00	0.00	3.27
131	132	0.472471	ACCAAACACCACCGTCTGAT	59.528	50.000	0.00	0.00	0.00	2.90
132	133	1.156736	CCAAACACCACCGTCTGATC	58.843	55.000	0.00	0.00	0.00	2.92
133	134	1.542328	CCAAACACCACCGTCTGATCA	60.542	52.381	0.00	0.00	0.00	2.92
134	135	2.426522	CAAACACCACCGTCTGATCAT	58.573	47.619	0.00	0.00	0.00	2.45
135	136	2.386661	AACACCACCGTCTGATCATC	57.613	50.000	0.00	0.00	0.00	2.92
136	137	1.266178	ACACCACCGTCTGATCATCA	58.734	50.000	0.00	0.00	0.00	3.07
149	151	6.800892	CGTCTGATCATCATCACTGTAGTATG	59.199	42.308	0.00	0.00	33.80	2.39
355	1886	1.005332	CAGAGACACCAGAGGGAGAGA	59.995	57.143	0.00	0.00	38.05	3.10
356	1887	1.284785	AGAGACACCAGAGGGAGAGAG	59.715	57.143	0.00	0.00	38.05	3.20
357	1888	1.283613	GAGACACCAGAGGGAGAGAGA	59.716	57.143	0.00	0.00	38.05	3.10
358	1889	1.284785	AGACACCAGAGGGAGAGAGAG	59.715	57.143	0.00	0.00	38.05	3.20
368	1899	2.509964	AGGGAGAGAGAGAGAGAGGTTC	59.490	54.545	0.00	0.00	0.00	3.62
451	1988	0.036010	ATGTCCCGGTGAAGCAAGAG	60.036	55.000	0.00	0.00	0.00	2.85
493	2030	1.301293	CCAAGGAAGAGGAGGTGGC	59.699	63.158	0.00	0.00	0.00	5.01
928	2492	0.387929	AAGCTCGACGACCACAAGAA	59.612	50.000	0.00	0.00	0.00	2.52
1045	2635	1.607756	AAGGTGCTCCAGCTCGAGA	60.608	57.895	18.75	0.00	41.59	4.04
1403	2996	2.681848	GCATTGACAAGATCACCTCCTG	59.318	50.000	0.00	0.00	36.92	3.86
1414	3007	4.967442	AGATCACCTCCTGAATGATTCTGA	59.033	41.667	12.83	4.60	33.21	3.27
1436	3029	5.481824	TGATATGCCTAGGGTTCTACTGATG	59.518	44.000	11.72	0.00	0.00	3.07
1445	3041	8.361139	CCTAGGGTTCTACTGATGTTAATACTG	58.639	40.741	0.00	0.00	0.00	2.74
1517	3127	1.004927	GGTAGCATGCGTCAATTCGTC	60.005	52.381	13.01	0.00	0.00	4.20
1579	3191	5.869888	CAGATGAGTACTTGTTAGTTCCCAC	59.130	44.000	0.00	0.00	35.78	4.61
1580	3192	5.542635	AGATGAGTACTTGTTAGTTCCCACA	59.457	40.000	0.00	0.00	35.78	4.17
1582	3194	5.547465	TGAGTACTTGTTAGTTCCCACATG	58.453	41.667	0.00	0.00	35.78	3.21
1698	3357	1.361668	CCCTCCACGTTCGCATTGAG	61.362	60.000	0.00	0.00	0.00	3.02
1991	5301	3.432326	GCATTAGAGGGGGTGTACTGAAG	60.432	52.174	0.00	0.00	0.00	3.02
1995	5305	0.192566	AGGGGGTGTACTGAAGTGGA	59.807	55.000	0.00	0.00	0.00	4.02
1996	5306	1.061546	GGGGGTGTACTGAAGTGGAA	58.938	55.000	0.00	0.00	0.00	3.53
1997	5307	1.271217	GGGGGTGTACTGAAGTGGAAC	60.271	57.143	0.00	0.00	0.00	3.62
1998	5308	1.271217	GGGGTGTACTGAAGTGGAACC	60.271	57.143	0.00	0.00	37.80	3.62
2150	5810	1.228644	TGCTGGCTCCAACATTGCT	60.229	52.632	0.00	0.00	0.00	3.91
2177	5838	1.244019	CCGCCCCAGTTTTCCTCTTG	61.244	60.000	0.00	0.00	0.00	3.02
2250	5911	5.000591	TGCGACCAGAAATAACAATGAAGA	58.999	37.500	0.00	0.00	0.00	2.87
2317	5978	1.962321	GAGTCGGAGAAAGGGGAGGC	61.962	65.000	0.00	0.00	39.69	4.70
2318	5979	2.121832	TCGGAGAAAGGGGAGGCA	59.878	61.111	0.00	0.00	0.00	4.75
2336	5997	1.148310	CAACGATGCAAGACGAAGGT	58.852	50.000	15.81	0.00	0.00	3.50

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
27	28	8.843262	GGTGCTTCTAAGGACTTTTAGTAAAAA	58.157	33.333	13.12	0.00	45.42	1.94
28	29	8.215736	AGGTGCTTCTAAGGACTTTTAGTAAAA	58.784	33.333	13.12	7.80	45.42	1.52
29	30	7.742767	AGGTGCTTCTAAGGACTTTTAGTAAA	58.257	34.615	13.12	0.00	45.42	2.01
30	31	7.312415	AGGTGCTTCTAAGGACTTTTAGTAA	57.688	36.000	13.12	0.00	45.42	2.24
31	32	6.930068	AGGTGCTTCTAAGGACTTTTAGTA	57.070	37.500	13.12	0.00	45.42	1.82
32	33	5.827326	AGGTGCTTCTAAGGACTTTTAGT	57.173	39.130	13.12	0.00	45.42	2.24
36	37	5.891551	TCAAAAAGGTGCTTCTAAGGACTTT	59.108	36.000	13.12	9.59	45.83	2.66
37	38	5.445964	TCAAAAAGGTGCTTCTAAGGACTT	58.554	37.500	13.12	3.95	45.42	3.01
38	39	5.048846	TCAAAAAGGTGCTTCTAAGGACT	57.951	39.130	13.12	0.00	45.42	3.85
39	40	5.063880	TCTCAAAAAGGTGCTTCTAAGGAC	58.936	41.667	5.86	5.86	45.39	3.85
40	41	5.163195	ACTCTCAAAAAGGTGCTTCTAAGGA	60.163	40.000	0.00	0.00	0.00	3.36
41	42	5.066593	ACTCTCAAAAAGGTGCTTCTAAGG	58.933	41.667	0.00	0.00	0.00	2.69
42	43	5.994668	AGACTCTCAAAAAGGTGCTTCTAAG	59.005	40.000	0.00	0.00	0.00	2.18
43	44	5.930135	AGACTCTCAAAAAGGTGCTTCTAA	58.070	37.500	0.00	0.00	0.00	2.10
44	45	5.552870	AGACTCTCAAAAAGGTGCTTCTA	57.447	39.130	0.00	0.00	0.00	2.10
45	46	4.429854	AGACTCTCAAAAAGGTGCTTCT	57.570	40.909	0.00	0.00	0.00	2.85
46	47	5.506686	AAAGACTCTCAAAAAGGTGCTTC	57.493	39.130	0.00	0.00	0.00	3.86
47	48	5.921962	AAAAGACTCTCAAAAAGGTGCTT	57.078	34.783	0.00	0.00	0.00	3.91
48	49	5.418840	TCAAAAAGACTCTCAAAAAGGTGCT	59.581	36.000	0.00	0.00	0.00	4.40
49	50	5.650543	TCAAAAAGACTCTCAAAAAGGTGC	58.349	37.500	0.00	0.00	0.00	5.01
50	51	8.532977	TTTTCAAAAAGACTCTCAAAAAGGTG	57.467	30.769	0.00	0.00	0.00	4.00
73	74	8.865420	GACTTTTTCTAGTCCCTAGGATTTTT	57.135	34.615	11.48	0.00	38.88	1.94
96	97	4.282703	TGTTTGGTTGTCTAGTCCTAGGAC	59.717	45.833	31.29	31.29	44.86	3.85
97	98	4.282703	GTGTTTGGTTGTCTAGTCCTAGGA	59.717	45.833	7.62	7.62	34.06	2.94
98	99	4.562963	GGTGTTTGGTTGTCTAGTCCTAGG	60.563	50.000	0.82	0.82	34.06	3.02
99	100	4.039973	TGGTGTTTGGTTGTCTAGTCCTAG	59.960	45.833	0.00	0.00	34.56	3.02
100	101	3.968649	TGGTGTTTGGTTGTCTAGTCCTA	59.031	43.478	0.00	0.00	0.00	2.94
101	102	2.775384	TGGTGTTTGGTTGTCTAGTCCT	59.225	45.455	0.00	0.00	0.00	3.85
102	103	2.876550	GTGGTGTTTGGTTGTCTAGTCC	59.123	50.000	0.00	0.00	0.00	3.85
103	104	2.876550	GGTGGTGTTTGGTTGTCTAGTC	59.123	50.000	0.00	0.00	0.00	2.59
104	105	2.743838	CGGTGGTGTTTGGTTGTCTAGT	60.744	50.000	0.00	0.00	0.00	2.57
105	106	1.871039	CGGTGGTGTTTGGTTGTCTAG	59.129	52.381	0.00	0.00	0.00	2.43
106	107	1.209990	ACGGTGGTGTTTGGTTGTCTA	59.790	47.619	0.00	0.00	0.00	2.59
107	108	0.034863	ACGGTGGTGTTTGGTTGTCT	60.035	50.000	0.00	0.00	0.00	3.41
108	109	0.379316	GACGGTGGTGTTTGGTTGTC	59.621	55.000	0.00	0.00	0.00	3.18
109	110	0.034863	AGACGGTGGTGTTTGGTTGT	60.035	50.000	0.00	0.00	0.00	3.32
110	111	0.380378	CAGACGGTGGTGTTTGGTTG	59.620	55.000	0.00	0.00	0.00	3.77
111	112	0.253610	TCAGACGGTGGTGTTTGGTT	59.746	50.000	0.00	0.00	0.00	3.67
112	113	0.472471	ATCAGACGGTGGTGTTTGGT	59.528	50.000	0.00	0.00	0.00	3.67
113	114	1.156736	GATCAGACGGTGGTGTTTGG	58.843	55.000	0.00	0.00	0.00	3.28
114	115	1.877637	TGATCAGACGGTGGTGTTTG	58.122	50.000	0.00	0.00	0.00	2.93
115	116	2.038426	TGATGATCAGACGGTGGTGTTT	59.962	45.455	0.09	0.00	0.00	2.83
116	117	1.623311	TGATGATCAGACGGTGGTGTT	59.377	47.619	0.09	0.00	0.00	3.32
117	118	1.266178	TGATGATCAGACGGTGGTGT	58.734	50.000	0.09	0.00	0.00	4.16
118	119	2.159057	TGATGATGATCAGACGGTGGTG	60.159	50.000	0.09	0.00	33.40	4.17
119	120	2.110578	TGATGATGATCAGACGGTGGT	58.889	47.619	0.09	0.00	33.40	4.16
120	121	2.102084	AGTGATGATGATCAGACGGTGG	59.898	50.000	0.09	0.00	39.36	4.61
121	122	3.121544	CAGTGATGATGATCAGACGGTG	58.878	50.000	0.09	0.00	39.36	4.94
122	123	2.762887	ACAGTGATGATGATCAGACGGT	59.237	45.455	0.09	4.52	39.36	4.83
123	124	3.449528	ACAGTGATGATGATCAGACGG	57.550	47.619	0.09	3.91	39.36	4.79
124	125	5.180367	ACTACAGTGATGATGATCAGACG	57.820	43.478	0.09	0.71	39.36	4.18
125	126	7.656412	ACATACTACAGTGATGATGATCAGAC	58.344	38.462	0.09	0.31	39.36	3.51
126	127	7.830099	ACATACTACAGTGATGATGATCAGA	57.170	36.000	0.09	0.00	39.36	3.27
127	128	7.598118	GGAACATACTACAGTGATGATGATCAG	59.402	40.741	0.09	0.00	39.36	2.90
128	129	7.436933	GGAACATACTACAGTGATGATGATCA	58.563	38.462	0.00	0.00	36.16	2.92
129	130	6.870965	GGGAACATACTACAGTGATGATGATC	59.129	42.308	0.00	0.00	0.00	2.92
130	131	6.239714	GGGGAACATACTACAGTGATGATGAT	60.240	42.308	0.00	0.00	0.00	2.45
131	132	5.070446	GGGGAACATACTACAGTGATGATGA	59.930	44.000	0.00	0.00	0.00	2.92
132	133	5.163311	TGGGGAACATACTACAGTGATGATG	60.163	44.000	0.00	0.00	0.00	3.07
133	134	4.968719	TGGGGAACATACTACAGTGATGAT	59.031	41.667	0.00	0.00	0.00	2.45
134	135	4.161565	GTGGGGAACATACTACAGTGATGA	59.838	45.833	0.00	0.00	0.00	2.92
135	136	4.442706	GTGGGGAACATACTACAGTGATG	58.557	47.826	0.00	0.00	0.00	3.07
136	137	3.454812	GGTGGGGAACATACTACAGTGAT	59.545	47.826	0.00	0.00	0.00	3.06
149	151	2.991540	GCTTGGCAGGTGGGGAAC	60.992	66.667	0.00	0.00	0.00	3.62
355	1886	2.442413	CTGGAACGAACCTCTCTCTCT	58.558	52.381	0.00	0.00	0.00	3.10
356	1887	1.474879	CCTGGAACGAACCTCTCTCTC	59.525	57.143	0.00	0.00	0.00	3.20
357	1888	1.551452	CCTGGAACGAACCTCTCTCT	58.449	55.000	0.00	0.00	0.00	3.10
358	1889	0.108567	GCCTGGAACGAACCTCTCTC	60.109	60.000	0.00	0.00	0.00	3.20
413	1950	0.627451	TTGAGATTGGGCAGCTCCAT	59.373	50.000	3.68	0.00	36.58	3.41
414	1951	0.627451	ATTGAGATTGGGCAGCTCCA	59.373	50.000	0.00	0.00	36.21	3.86
415	1952	1.030457	CATTGAGATTGGGCAGCTCC	58.970	55.000	0.00	0.00	0.00	4.70
416	1953	1.674962	GACATTGAGATTGGGCAGCTC	59.325	52.381	0.00	0.00	0.00	4.09
417	1954	1.684248	GGACATTGAGATTGGGCAGCT	60.684	52.381	0.00	0.00	0.00	4.24
418	1955	0.743097	GGACATTGAGATTGGGCAGC	59.257	55.000	0.00	0.00	0.00	5.25
451	1988	4.553547	GCTCCTTCATTATGCACAACGATC	60.554	45.833	0.00	0.00	0.00	3.69
1136	2726	2.264480	CCACCGACAAGGCGATGA	59.736	61.111	0.00	0.00	46.52	2.92
1222	2815	4.680237	CCTGTCGTTGCCTGCCGA	62.680	66.667	0.00	0.00	0.00	5.54
1227	2820	2.915659	TCGGTCCTGTCGTTGCCT	60.916	61.111	0.00	0.00	0.00	4.75
1229	2822	2.028484	TGTCGGTCCTGTCGTTGC	59.972	61.111	0.00	0.00	0.00	4.17
1255	2848	0.246635	CTCGTCACCTGGATTTCCGT	59.753	55.000	0.00	0.00	39.43	4.69
1364	2957	1.078426	CGAACATGGAGGGACACCC	60.078	63.158	0.00	0.00	45.90	4.61
1403	2996	6.059787	ACCCTAGGCATATCAGAATCATTC	57.940	41.667	2.05	0.00	0.00	2.67
1414	3007	5.407049	ACATCAGTAGAACCCTAGGCATAT	58.593	41.667	2.05	0.00	0.00	1.78
1445	3041	9.559732	TTAAACCAAACTAGACTAAACCTTACC	57.440	33.333	0.00	0.00	0.00	2.85
1540	3150	6.698008	ACTCATCTGATGTTTTCACACAAA	57.302	33.333	16.66	0.00	35.03	2.83
1555	3167	5.869888	GTGGGAACTAACAAGTACTCATCTG	59.130	44.000	0.00	0.00	0.00	2.90
1579	3191	8.424918	AAGATACCTCTTCCATGTACTAACATG	58.575	37.037	10.79	10.79	45.58	3.21
1580	3192	8.424918	CAAGATACCTCTTCCATGTACTAACAT	58.575	37.037	0.00	0.00	42.24	2.71
1582	3194	7.707035	CACAAGATACCTCTTCCATGTACTAAC	59.293	40.741	0.00	0.00	39.78	2.34
1698	3357	3.243569	CGGGTCAGACTATGGTGATCTTC	60.244	52.174	0.00	0.00	0.00	2.87
1888	5171	8.859236	AACTCACAATATGGGATATGATCTTG	57.141	34.615	0.00	0.00	30.75	3.02
1991	5301	6.607019	TGGGATAATATAACTTGGGTTCCAC	58.393	40.000	0.00	0.00	36.92	4.02
2250	5911	1.415672	TTGCCACGACTCTCCCCTTT	61.416	55.000	0.00	0.00	0.00	3.11
2317	5978	1.136252	CACCTTCGTCTTGCATCGTTG	60.136	52.381	0.00	0.00	0.00	4.10
2318	5979	1.148310	CACCTTCGTCTTGCATCGTT	58.852	50.000	0.00	0.00	0.00	3.85
2327	5988	1.674057	CCCTGCTTCACCTTCGTCT	59.326	57.895	0.00	0.00	0.00	4.18

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.