AutoCloner

Multiple sequence alignment - TraesCS1A01G004600

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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	TraesCS1A01G004600	chr1A	100.000	8969	0	0	1	8969	2844877	2835909	0.000000e+00	16563.0
1	TraesCS1A01G004600	chr1A	84.934	1354	142	17	3219	4545	2657577	2656259	0.000000e+00	1314.0
2	TraesCS1A01G004600	chr1A	79.556	900	130	32	1843	2699	2647087	2646199	2.160000e-165	593.0
3	TraesCS1A01G004600	chr1A	84.452	566	49	21	5409	5943	2643803	2643246	1.030000e-143	521.0
4	TraesCS1A01G004600	chr1A	84.632	462	43	11	1023	1464	2647821	2647368	1.380000e-117	435.0
5	TraesCS1A01G004600	chr1A	81.693	508	67	12	7426	7907	2653560	2653053	5.040000e-107	399.0
6	TraesCS1A01G004600	chr1A	94.606	241	10	2	4879	5119	2826170	2825933	3.960000e-98	370.0
7	TraesCS1A01G004600	chr1A	85.294	340	47	3	5825	6161	2653965	2653626	1.850000e-91	348.0
8	TraesCS1A01G004600	chr1A	84.127	378	33	9	2829	3197	2646189	2645830	3.100000e-89	340.0
9	TraesCS1A01G004600	chr1A	84.911	338	36	7	5079	5407	2655781	2655450	2.410000e-85	327.0
10	TraesCS1A01G004600	chr1A	85.268	224	22	5	5188	5405	2644073	2643855	4.220000e-53	220.0
11	TraesCS1A01G004600	chr1A	87.568	185	19	2	7408	7588	2643006	2642822	2.540000e-50	211.0
12	TraesCS1A01G004600	chr1A	90.345	145	14	0	6584	6728	251947529	251947673	3.310000e-44	191.0
13	TraesCS1A01G004600	chr1A	86.047	172	21	3	3508	3676	2645382	2645211	1.990000e-41	182.0
14	TraesCS1A01G004600	chr1A	78.049	246	42	6	5078	5316	2663818	2663578	2.610000e-30	145.0
15	TraesCS1A01G004600	chr1A	82.069	145	15	6	3675	3819	2645238	2645105	7.360000e-21	113.0
16	TraesCS1A01G004600	chr1A	100.000	35	0	0	8632	8666	587934492	587934458	2.090000e-06	65.8
17	TraesCS1A01G004600	chr6D	95.806	5150	135	22	996	6138	472430113	472425038	0.000000e+00	8239.0
18	TraesCS1A01G004600	chr6D	93.516	1789	79	10	6137	7916	472424994	472423234	0.000000e+00	2627.0
19	TraesCS1A01G004600	chr6D	90.909	1001	86	5	1	998	119841673	119840675	0.000000e+00	1339.0
20	TraesCS1A01G004600	chr6D	81.445	1412	174	50	1843	3205	472501562	472500190	0.000000e+00	1075.0
21	TraesCS1A01G004600	chr6D	90.330	455	19	2	8515	8969	472422970	472422541	2.810000e-159	573.0
22	TraesCS1A01G004600	chr6D	84.982	566	46	19	5409	5943	472498059	472497502	1.020000e-148	538.0
23	TraesCS1A01G004600	chr6D	90.938	320	26	3	6269	6586	472958228	472957910	2.310000e-115	427.0
24	TraesCS1A01G004600	chr6D	80.157	635	67	19	3206	3819	472499955	472499359	3.870000e-113	420.0
25	TraesCS1A01G004600	chr6D	91.379	290	24	1	7120	7409	124947668	124947380	6.530000e-106	396.0
26	TraesCS1A01G004600	chr6D	79.794	485	69	16	7950	8422	472496705	472496238	8.680000e-85	326.0
27	TraesCS1A01G004600	chr6D	77.718	561	90	19	5575	6130	472489198	472488668	2.430000e-80	311.0
28	TraesCS1A01G004600	chr6D	84.887	311	41	5	6727	7034	320203995	320203688	8.750000e-80	309.0
29	TraesCS1A01G004600	chr6D	94.194	155	9	0	8357	8511	472423188	472423034	4.190000e-58	237.0
30	TraesCS1A01G004600	chr6D	92.405	158	12	0	1053	1210	472491908	472491751	9.060000e-55	226.0
31	TraesCS1A01G004600	chr6D	88.108	185	18	2	7408	7588	472497264	472497080	5.450000e-52	217.0
32	TraesCS1A01G004600	chr6D	94.318	88	5	0	8421	8508	318237511	318237598	1.570000e-27	135.0
33	TraesCS1A01G004600	chr6D	93.103	87	6	0	8422	8508	36996359	36996273	2.630000e-25	128.0
34	TraesCS1A01G004600	chr6D	92.222	90	7	0	8419	8508	106557831	106557920	2.630000e-25	128.0
35	TraesCS1A01G004600	chr6D	92.222	90	7	0	8419	8508	113135745	113135834	2.630000e-25	128.0
36	TraesCS1A01G004600	chr6D	89.583	96	10	0	8422	8517	314191133	314191038	1.220000e-23	122.0
37	TraesCS1A01G004600	chr6D	100.000	34	0	0	7912	7945	472423220	472423187	7.520000e-06	63.9
38	TraesCS1A01G004600	chr6A	95.616	4790	156	19	3504	8254	617555170	617559944	0.000000e+00	7633.0
39	TraesCS1A01G004600	chr6A	96.847	2474	67	8	993	3465	617552385	617554848	0.000000e+00	4126.0
40	TraesCS1A01G004600	chr6A	83.426	1261	131	23	3292	4547	617320648	617321835	0.000000e+00	1099.0
41	TraesCS1A01G004600	chr6A	95.725	655	17	4	8323	8969	617559949	617560600	0.000000e+00	1044.0
42	TraesCS1A01G004600	chr6A	87.306	772	76	11	3785	4545	617237655	617238415	0.000000e+00	863.0
43	TraesCS1A01G004600	chr6A	84.675	770	96	8	3784	4545	617224235	617224990	0.000000e+00	749.0
44	TraesCS1A01G004600	chr6A	85.781	647	76	10	5530	6161	617351752	617352397	0.000000e+00	671.0
45	TraesCS1A01G004600	chr6A	81.094	841	115	25	1911	2716	617319021	617319852	4.570000e-177	632.0
46	TraesCS1A01G004600	chr6A	81.701	776	93	14	2264	3020	617349248	617349993	1.290000e-167	601.0
47	TraesCS1A01G004600	chr6A	84.043	564	52	18	5409	5943	617322413	617322967	8.030000e-140	508.0
48	TraesCS1A01G004600	chr6A	84.241	514	60	8	7408	7904	617323205	617323714	1.750000e-131	481.0
49	TraesCS1A01G004600	chr6A	85.232	474	60	2	3304	3777	617237217	617237680	6.300000e-131	479.0
50	TraesCS1A01G004600	chr6A	84.200	500	57	8	7427	7904	617240058	617240557	4.900000e-127	466.0
51	TraesCS1A01G004600	chr6A	86.634	404	52	2	4143	4545	617350450	617350852	6.390000e-121	446.0
52	TraesCS1A01G004600	chr6A	85.581	430	43	12	2780	3197	617319875	617320297	4.970000e-117	433.0
53	TraesCS1A01G004600	chr6A	81.148	488	76	12	2728	3201	617236346	617236831	2.360000e-100	377.0
54	TraesCS1A01G004600	chr6A	82.989	435	48	8	1020	1429	617318232	617318665	3.960000e-98	370.0
55	TraesCS1A01G004600	chr6A	93.061	245	17	0	5576	5820	617239443	617239687	8.560000e-95	359.0
56	TraesCS1A01G004600	chr6A	75.558	806	137	37	1874	2634	617235517	617236307	8.620000e-90	342.0
57	TraesCS1A01G004600	chr6A	80.000	480	65	14	7953	8422	617323844	617324302	8.680000e-85	326.0
58	TraesCS1A01G004600	chr6A	82.891	339	36	14	1020	1344	617217532	617217862	1.470000e-72	285.0
59	TraesCS1A01G004600	chr6A	83.912	317	31	8	1144	1448	617234884	617235192	1.470000e-72	285.0
60	TraesCS1A01G004600	chr6A	90.431	209	19	1	5078	5286	617351327	617351534	3.190000e-69	274.0
61	TraesCS1A01G004600	chr6A	87.603	242	19	8	5920	6155	617239749	617239985	4.130000e-68	270.0
62	TraesCS1A01G004600	chr6A	88.649	185	21	0	2449	2633	617222978	617223162	9.060000e-55	226.0
63	TraesCS1A01G004600	chr6A	81.855	248	36	8	2151	2394	617341872	617342114	5.490000e-47	200.0
64	TraesCS1A01G004600	chr6A	84.018	219	22	6	5195	5407	617239011	617239222	1.980000e-46	198.0
65	TraesCS1A01G004600	chr6A	87.500	152	19	0	8515	8666	351703380	351703531	9.250000e-40	176.0
66	TraesCS1A01G004600	chr6A	80.000	240	36	7	5078	5309	617343556	617343791	5.570000e-37	167.0
67	TraesCS1A01G004600	chr6A	95.402	87	4	0	8422	8508	351703226	351703312	1.210000e-28	139.0
68	TraesCS1A01G004600	chr6A	94.444	90	4	1	8422	8511	23854374	23854286	4.370000e-28	137.0
69	TraesCS1A01G004600	chr6A	81.905	105	19	0	1661	1765	617218153	617218257	1.240000e-13	89.8
70	TraesCS1A01G004600	chr6B	95.089	3441	100	14	2344	5766	717141703	717138314	0.000000e+00	5354.0
71	TraesCS1A01G004600	chr6B	90.761	920	38	9	7177	8062	717137905	717136999	0.000000e+00	1184.0
72	TraesCS1A01G004600	chr6B	87.663	997	96	9	3556	4545	717401647	717400671	0.000000e+00	1134.0
73	TraesCS1A01G004600	chr6B	94.523	639	29	5	1722	2359	717142379	717141746	0.000000e+00	981.0
74	TraesCS1A01G004600	chr6B	94.206	466	25	2	993	1458	717143154	717142691	0.000000e+00	710.0
75	TraesCS1A01G004600	chr6B	85.757	667	73	6	3885	4547	717417789	717417141	0.000000e+00	686.0
76	TraesCS1A01G004600	chr6B	94.470	434	23	1	8078	8511	717116252	717115820	0.000000e+00	667.0
77	TraesCS1A01G004600	chr6B	85.781	640	71	11	5530	6161	717399634	717399007	0.000000e+00	660.0
78	TraesCS1A01G004600	chr6B	80.221	905	127	29	1843	2706	717419688	717418795	4.570000e-177	632.0
79	TraesCS1A01G004600	chr6B	91.106	416	35	2	6714	7128	717138317	717137903	6.080000e-156	562.0
80	TraesCS1A01G004600	chr6B	88.571	455	27	4	8515	8969	717115756	717115327	6.170000e-146	529.0
81	TraesCS1A01G004600	chr6B	86.237	465	45	10	5409	5862	717416249	717415793	3.760000e-133	486.0
82	TraesCS1A01G004600	chr6B	87.119	427	41	6	2780	3197	717418764	717418343	1.050000e-128	472.0
83	TraesCS1A01G004600	chr6B	83.236	513	65	8	7408	7903	717415435	717414927	1.370000e-122	451.0
84	TraesCS1A01G004600	chr6B	82.025	484	59	17	7950	8422	717414799	717414333	3.930000e-103	387.0
85	TraesCS1A01G004600	chr6B	85.460	337	43	6	3291	3621	717401958	717401622	6.670000e-91	346.0
86	TraesCS1A01G004600	chr6B	83.548	310	47	3	6724	7029	544764348	544764039	4.100000e-73	287.0
87	TraesCS1A01G004600	chr6B	82.591	247	32	8	2151	2394	717411183	717410945	3.280000e-49	207.0
88	TraesCS1A01G004600	chr6B	95.833	120	5	0	1456	1575	717142588	717142469	2.560000e-45	195.0
89	TraesCS1A01G004600	chr6B	87.209	172	18	2	4684	4851	717400415	717400244	9.190000e-45	193.0
90	TraesCS1A01G004600	chr6B	78.947	266	51	5	5897	6157	717408005	717407740	9.250000e-40	176.0
91	TraesCS1A01G004600	chr6B	89.552	134	13	1	4547	4679	717417079	717416946	1.550000e-37	169.0
92	TraesCS1A01G004600	chr6B	86.897	145	18	1	3675	3819	717417963	717417820	2.590000e-35	161.0
93	TraesCS1A01G004600	chr6B	94.444	54	3	0	3581	3634	717418028	717417975	5.770000e-12	84.2
94	TraesCS1A01G004600	chr1D	91.708	1001	80	3	1	998	250092477	250093477	0.000000e+00	1386.0
95	TraesCS1A01G004600	chr1D	89.655	174	17	1	4877	5050	365430345	365430517	4.220000e-53	220.0
96	TraesCS1A01G004600	chr1D	89.143	175	16	3	4877	5049	9867807	9867634	1.960000e-51	215.0
97	TraesCS1A01G004600	chr1D	94.444	90	5	0	8422	8511	254578748	254578659	1.210000e-28	139.0
98	TraesCS1A01G004600	chr1D	91.176	102	6	3	8409	8508	431522107	431522207	1.570000e-27	135.0
99	TraesCS1A01G004600	chr1D	93.333	90	6	0	8422	8511	111848521	111848432	5.650000e-27	134.0
100	TraesCS1A01G004600	chr1D	92.553	94	6	1	8418	8511	392090045	392089953	5.650000e-27	134.0
101	TraesCS1A01G004600	chr1D	89.524	105	11	0	6163	6267	486311121	486311017	5.650000e-27	134.0
102	TraesCS1A01G004600	chr1D	74.834	151	31	4	8518	8666	238653070	238653215	2.700000e-05	62.1
103	TraesCS1A01G004600	chr4D	91.409	1001	81	5	1	998	232048477	232049475	0.000000e+00	1367.0
104	TraesCS1A01G004600	chr4D	91.000	1000	83	4	1	998	313739751	313740745	0.000000e+00	1341.0
105	TraesCS1A01G004600	chr7D	91.009	1001	85	5	1	998	60611765	60610767	0.000000e+00	1345.0
106	TraesCS1A01G004600	chr7D	84.295	312	44	4	6726	7033	592686830	592687140	5.260000e-77	300.0
107	TraesCS1A01G004600	chr7D	90.230	174	15	2	4877	5049	5318785	5318957	9.060000e-55	226.0
108	TraesCS1A01G004600	chr7D	95.556	90	4	0	8419	8508	315667100	315667189	2.610000e-30	145.0
109	TraesCS1A01G004600	chr7D	81.481	135	24	1	8532	8666	445447419	445447286	9.520000e-20	110.0
110	TraesCS1A01G004600	chr7D	89.394	66	6	1	7028	7093	157679887	157679951	2.080000e-11	82.4
111	TraesCS1A01G004600	chr5D	91.000	1000	87	3	1	998	480622683	480621685	0.000000e+00	1345.0
112	TraesCS1A01G004600	chr5D	91.000	1000	85	4	1	998	480668741	480667745	0.000000e+00	1343.0
113	TraesCS1A01G004600	chr5D	91.667	300	23	2	7111	7409	210677899	210678197	1.800000e-111	414.0
114	TraesCS1A01G004600	chr5D	83.172	309	45	6	6727	7029	545768428	545768121	8.870000e-70	276.0
115	TraesCS1A01G004600	chr5D	93.421	152	9	1	8515	8666	221824424	221824274	3.260000e-54	224.0
116	TraesCS1A01G004600	chr5D	95.604	91	4	0	8421	8511	221824578	221824488	7.260000e-31	147.0
117	TraesCS1A01G004600	chr5D	92.553	94	6	1	8418	8511	176380133	176380225	5.650000e-27	134.0
118	TraesCS1A01G004600	chr5D	90.476	63	5	1	7028	7090	454109339	454109278	2.080000e-11	82.4
119	TraesCS1A01G004600	chr3D	90.900	1000	89	2	1	998	374293745	374292746	0.000000e+00	1341.0
120	TraesCS1A01G004600	chr3D	90.828	1003	85	7	1	998	356709724	356710724	0.000000e+00	1336.0
121	TraesCS1A01G004600	chr3D	90.816	294	27	0	7120	7413	175803370	175803077	2.350000e-105	394.0
122	TraesCS1A01G004600	chr3D	90.476	294	28	0	7120	7413	176089964	176089671	1.090000e-103	388.0
123	TraesCS1A01G004600	chr3D	92.442	172	11	2	4877	5047	580128345	580128515	2.500000e-60	244.0
124	TraesCS1A01G004600	chr3D	93.407	91	6	0	8418	8508	420987233	420987323	1.570000e-27	135.0
125	TraesCS1A01G004600	chr3D	89.524	105	11	0	6163	6267	5847037	5846933	5.650000e-27	134.0
126	TraesCS1A01G004600	chr3D	100.000	28	0	0	8637	8664	145055032	145055005	1.600000e-02	52.8
127	TraesCS1A01G004600	chr4B	90.566	318	27	3	6269	6584	171806343	171806027	1.390000e-112	418.0
128	TraesCS1A01G004600	chr4B	93.333	90	6	0	8419	8508	369624568	369624657	5.650000e-27	134.0
129	TraesCS1A01G004600	chr4B	93.333	90	6	0	8422	8511	625701497	625701408	5.650000e-27	134.0
130	TraesCS1A01G004600	chr2D	89.735	302	30	1	7110	7411	510229987	510230287	1.410000e-102	385.0
131	TraesCS1A01G004600	chr2D	85.099	302	40	5	6721	7018	154184981	154185281	4.070000e-78	303.0
132	TraesCS1A01G004600	chr2D	83.117	308	44	7	6727	7029	13621681	13621377	3.190000e-69	274.0
133	TraesCS1A01G004600	chr2D	93.103	145	10	0	6584	6728	375814383	375814527	7.050000e-51	213.0
134	TraesCS1A01G004600	chr2D	89.655	145	15	0	6584	6728	373745363	373745507	1.540000e-42	185.0
135	TraesCS1A01G004600	chr2D	89.655	145	15	0	6584	6728	490559030	490559174	1.540000e-42	185.0
136	TraesCS1A01G004600	chr1B	89.933	298	28	2	7120	7417	70452010	70451715	5.080000e-102	383.0
137	TraesCS1A01G004600	chr1B	94.505	91	5	0	8418	8508	667612815	667612905	3.380000e-29	141.0
138	TraesCS1A01G004600	chr1B	90.566	106	9	1	6163	6267	185537165	185537270	1.210000e-28	139.0
139	TraesCS1A01G004600	chr1B	81.034	116	21	1	8551	8666	334899838	334899724	3.450000e-14	91.6
140	TraesCS1A01G004600	chr1B	100.000	32	0	0	8635	8666	30458005	30458036	9.720000e-05	60.2
141	TraesCS1A01G004600	chr2B	84.192	291	40	5	6727	7013	762217754	762218042	2.470000e-70	278.0
142	TraesCS1A01G004600	chr2B	89.655	145	15	0	6584	6728	50023777	50023921	1.540000e-42	185.0
143	TraesCS1A01G004600	chr2B	93.103	58	4	0	7028	7085	443209667	443209724	1.600000e-12	86.1
144	TraesCS1A01G004600	chr2B	89.231	65	5	2	7028	7092	451835075	451835013	7.460000e-11	80.5
145	TraesCS1A01G004600	chr2B	85.333	75	10	1	8592	8666	370880561	370880488	9.660000e-10	76.8
146	TraesCS1A01G004600	chr3A	89.474	171	16	2	4877	5046	697287328	697287159	1.960000e-51	215.0
147	TraesCS1A01G004600	chr3A	89.720	107	11	0	6161	6267	26190888	26190782	4.370000e-28	137.0
148	TraesCS1A01G004600	chr4A	90.345	145	14	0	6584	6728	554647273	554647129	3.310000e-44	191.0
149	TraesCS1A01G004600	chr4A	89.655	145	15	0	6584	6728	568147571	568147715	1.540000e-42	185.0
150	TraesCS1A01G004600	chr4A	82.963	135	21	2	8532	8666	205496833	205496701	4.400000e-23	121.0
151	TraesCS1A01G004600	chr4A	83.750	80	10	3	7028	7107	209332158	209332234	1.250000e-08	73.1
152	TraesCS1A01G004600	chr3B	91.429	105	9	0	6163	6267	507737786	507737890	2.610000e-30	145.0
153	TraesCS1A01G004600	chr3B	95.556	90	4	0	8422	8511	627977315	627977226	2.610000e-30	145.0
154	TraesCS1A01G004600	chr3B	91.509	106	5	3	8407	8511	229506703	229506601	9.390000e-30	143.0
155	TraesCS1A01G004600	chr3B	86.667	75	9	1	8592	8666	249823858	249823785	2.080000e-11	82.4
156	TraesCS1A01G004600	chrUn	95.506	89	4	0	8420	8508	103496586	103496674	9.390000e-30	143.0
157	TraesCS1A01G004600	chrUn	93.103	87	6	0	8422	8508	98632744	98632658	2.630000e-25	128.0
158	TraesCS1A01G004600	chrUn	92.222	90	7	0	8419	8508	308124116	308124205	2.630000e-25	128.0
159	TraesCS1A01G004600	chrUn	89.691	97	10	0	8421	8517	33304422	33304326	3.400000e-24	124.0
160	TraesCS1A01G004600	chrUn	91.111	90	8	0	8419	8508	3401279	3401368	1.220000e-23	122.0
161	TraesCS1A01G004600	chrUn	91.209	91	7	1	8419	8508	6368847	6368937	1.220000e-23	122.0
162	TraesCS1A01G004600	chrUn	92.045	88	6	1	8422	8508	19964675	19964588	1.220000e-23	122.0
163	TraesCS1A01G004600	chrUn	91.209	91	7	1	8419	8508	53812377	53812467	1.220000e-23	122.0
164	TraesCS1A01G004600	chrUn	91.209	91	7	1	8419	8508	63705465	63705555	1.220000e-23	122.0
165	TraesCS1A01G004600	chr7B	90.654	107	10	0	6161	6267	79316889	79316783	9.390000e-30	143.0
166	TraesCS1A01G004600	chr7B	93.750	96	5	1	8416	8511	313152763	313152669	9.390000e-30	143.0
167	TraesCS1A01G004600	chr7B	89.524	105	11	0	6163	6267	41328115	41328011	5.650000e-27	134.0
168	TraesCS1A01G004600	chr7B	93.103	58	3	1	7028	7085	720069884	720069940	5.770000e-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	TraesCS1A01G004600	chr1A	2835909	2844877	8968	True	16563.000000	16563	100.000000	1	8969	1	chr1A.!!$R3	8968
1	TraesCS1A01G004600	chr1A	2653053	2657577	4524	True	597.000000	1314	84.208000	3219	7907	4	chr1A.!!$R6	4688
2	TraesCS1A01G004600	chr1A	2642822	2647821	4999	True	326.875000	593	84.214875	1023	7588	8	chr1A.!!$R5	6565
3	TraesCS1A01G004600	chr6D	472422541	472430113	7572	True	2347.980000	8239	94.769200	996	8969	5	chr6D.!!$R7	7973
4	TraesCS1A01G004600	chr6D	119840675	119841673	998	True	1339.000000	1339	90.909000	1	998	1	chr6D.!!$R2	997
5	TraesCS1A01G004600	chr6D	472496238	472501562	5324	True	515.200000	1075	82.897200	1843	8422	5	chr6D.!!$R9	6579
6	TraesCS1A01G004600	chr6D	472488668	472491908	3240	True	268.500000	311	85.061500	1053	6130	2	chr6D.!!$R8	5077
7	TraesCS1A01G004600	chr6A	617552385	617560600	8215	False	4267.666667	7633	96.062667	993	8969	3	chr6A.!!$F8	7976
8	TraesCS1A01G004600	chr6A	617318232	617324302	6070	False	549.857143	1099	83.053429	1020	8422	7	chr6A.!!$F5	7402
9	TraesCS1A01G004600	chr6A	617349248	617352397	3149	False	498.000000	671	86.136750	2264	6161	4	chr6A.!!$F7	3897
10	TraesCS1A01G004600	chr6A	617222978	617224990	2012	False	487.500000	749	86.662000	2449	4545	2	chr6A.!!$F3	2096
11	TraesCS1A01G004600	chr6A	617234884	617240557	5673	False	404.333333	863	84.670889	1144	7904	9	chr6A.!!$F4	6760
12	TraesCS1A01G004600	chr6B	717136999	717143154	6155	True	1497.666667	5354	93.586333	993	8062	6	chr6B.!!$R3	7069
13	TraesCS1A01G004600	chr6B	717115327	717116252	925	True	598.000000	667	91.520500	8078	8969	2	chr6B.!!$R2	891
14	TraesCS1A01G004600	chr6B	717399007	717401958	2951	True	583.250000	1134	86.528250	3291	6161	4	chr6B.!!$R4	2870
15	TraesCS1A01G004600	chr6B	717407740	717419688	11948	True	355.563636	686	85.184182	1843	8422	11	chr6B.!!$R5	6579
16	TraesCS1A01G004600	chr1D	250092477	250093477	1000	False	1386.000000	1386	91.708000	1	998	1	chr1D.!!$F2	997
17	TraesCS1A01G004600	chr4D	232048477	232049475	998	False	1367.000000	1367	91.409000	1	998	1	chr4D.!!$F1	997
18	TraesCS1A01G004600	chr4D	313739751	313740745	994	False	1341.000000	1341	91.000000	1	998	1	chr4D.!!$F2	997
19	TraesCS1A01G004600	chr7D	60610767	60611765	998	True	1345.000000	1345	91.009000	1	998	1	chr7D.!!$R1	997
20	TraesCS1A01G004600	chr5D	480621685	480622683	998	True	1345.000000	1345	91.000000	1	998	1	chr5D.!!$R2	997
21	TraesCS1A01G004600	chr5D	480667745	480668741	996	True	1343.000000	1343	91.000000	1	998	1	chr5D.!!$R3	997
22	TraesCS1A01G004600	chr3D	374292746	374293745	999	True	1341.000000	1341	90.900000	1	998	1	chr3D.!!$R5	997
23	TraesCS1A01G004600	chr3D	356709724	356710724	1000	False	1336.000000	1336	90.828000	1	998	1	chr3D.!!$F1	997

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
764	771	0.558712	TTAACTTGGGGTGCCTTGGT	59.441	50.000	0.00	0.0	0.00	3.67	F
1154	1162	0.389948	GCCTCACCGACGACTTCAAT	60.390	55.000	0.00	0.0	0.00	2.57	F
1300	1322	1.314730	GATTTGTGTTGGGTGGTCGT	58.685	50.000	0.00	0.0	0.00	4.34	F
1627	1953	2.147958	TCGTGCGCCATTACTCTTTTT	58.852	42.857	4.18	0.0	0.00	1.94	F
3456	4441	2.686915	AGTATCACTAACGAGGGTTCCG	59.313	50.000	0.00	0.0	37.58	4.30	F
4556	6370	1.072806	TCCTGAAACATGACAGCTGCT	59.927	47.619	15.27	0.0	33.40	4.24	F
6289	9615	1.336125	GGCATCTACAATGCAAGAGCC	59.664	52.381	11.69	0.7	46.21	4.70	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1957	2293	0.240945	AATTTTGCCTGCGGTTCTCG	59.759	50.000	0.00	42.76	4.04	R
2502	2983	2.497273	GGGACATAAAGGCAGCAACATT	59.503	45.455	0.00	0.00	2.71	R
3266	4229	4.404073	AGCAGTCTAGCAAACTAGCAGTAT	59.596	41.667	0.00	44.83	2.12	R
3502	4489	5.400066	AGGTTGATAAAACAAAATCCCCG	57.600	39.130	0.00	0.00	5.73	R
4923	6927	1.287815	CACTACCGCCGTCAGAACA	59.712	57.895	0.00	0.00	3.18	R
6349	9675	1.146152	TCCTCCGTTGGGGAAACAAAT	59.854	47.619	0.00	46.61	2.32	R
8003	11464	0.250597	GGGCCTTACGCGGGATAAAT	60.251	55.000	12.47	38.94	1.40	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
31	32	7.123247	ACTTCTTGAAATATTGTCTTGGGATGG	59.877	37.037	0.00	0.00	0.00	3.51
38	39	1.139498	TGTCTTGGGATGGCTTGGGA	61.139	55.000	0.00	0.00	0.00	4.37
41	42	1.362237	TCTTGGGATGGCTTGGGAATT	59.638	47.619	0.00	0.00	0.00	2.17
74	75	6.061441	TGAGCTTTTGTGTCTCCTTAATTCA	58.939	36.000	0.00	0.00	0.00	2.57
77	78	7.373493	AGCTTTTGTGTCTCCTTAATTCATTG	58.627	34.615	0.00	0.00	0.00	2.82
123	124	8.527567	TCTTAAAAACTTCAACCACACAAAAG	57.472	30.769	0.00	0.00	0.00	2.27
171	173	9.691362	AGTTAGTATAAACCAATGCAAAAACTG	57.309	29.630	0.00	0.00	0.00	3.16
236	238	5.439721	ACATTGCATACTAAATGCCTCTGA	58.560	37.500	7.46	0.00	43.94	3.27
319	322	5.590530	AACAATCTGCCAAAACAGTACAA	57.409	34.783	0.00	0.00	38.84	2.41
336	339	8.340618	ACAGTACAATCTGTAAAGAATGCAAT	57.659	30.769	0.00	0.00	45.31	3.56
456	459	6.292923	TCACATTCTAACTTTTCTCGGGAAA	58.707	36.000	6.31	6.31	39.38	3.13
460	463	8.297426	ACATTCTAACTTTTCTCGGGAAATTTC	58.703	33.333	12.07	9.83	40.57	2.17
573	579	9.731519	GAAAAGAAAGATGCAAAACATTTATCG	57.268	29.630	0.00	0.00	39.84	2.92
663	669	7.610305	ACGAATAAAAATGTAGGTCCAAGTGAT	59.390	33.333	0.00	0.00	0.00	3.06
676	682	5.820947	GGTCCAAGTGATGTTACCGATAATT	59.179	40.000	0.00	0.00	0.00	1.40
764	771	0.558712	TTAACTTGGGGTGCCTTGGT	59.441	50.000	0.00	0.00	0.00	3.67
766	773	2.672996	CTTGGGGTGCCTTGGTCG	60.673	66.667	0.00	0.00	0.00	4.79
777	784	1.446272	CTTGGTCGTCCCGAAGCTC	60.446	63.158	0.00	0.00	37.72	4.09
816	823	6.948309	TCCTTATTCTCCTCATATCGACATCA	59.052	38.462	0.00	0.00	0.00	3.07
903	911	4.155826	TGATAAGGAGCAAACCATTTCACG	59.844	41.667	0.00	0.00	0.00	4.35
919	927	2.828877	TCACGTTGGTACTGTCAAAGG	58.171	47.619	0.00	0.00	0.00	3.11
948	956	8.587608	AGATTCATAATTGTTTCCACACAATGT	58.412	29.630	0.00	0.00	44.95	2.71
1037	1045	2.297895	AAGTATGACGGGGCAGGCA	61.298	57.895	0.00	0.00	0.00	4.75
1154	1162	0.389948	GCCTCACCGACGACTTCAAT	60.390	55.000	0.00	0.00	0.00	2.57
1252	1274	1.758440	GATCCGCATCCACCCTAGCA	61.758	60.000	0.00	0.00	0.00	3.49
1300	1322	1.314730	GATTTGTGTTGGGTGGTCGT	58.685	50.000	0.00	0.00	0.00	4.34
1627	1953	2.147958	TCGTGCGCCATTACTCTTTTT	58.852	42.857	4.18	0.00	0.00	1.94
1638	1964	5.277779	CCATTACTCTTTTTCGTGTGAAGCA	60.278	40.000	0.00	0.00	35.06	3.91
1741	2067	5.257082	TGCGTGTGAAGCTTATAGTGATA	57.743	39.130	0.00	0.00	35.28	2.15
1765	2091	4.584029	ATCTCAATAAGTTGTTGACGCG	57.416	40.909	10.66	3.53	36.69	6.01
1778	2104	5.009048	TGTTGACGCGTACAGTTAATTTC	57.991	39.130	13.97	0.00	0.00	2.17
1780	2106	5.006455	TGTTGACGCGTACAGTTAATTTCAA	59.994	36.000	13.97	4.41	0.00	2.69
1957	2293	6.260050	TGATTCGTGAGCCCATTACTTTTATC	59.740	38.462	0.00	0.00	0.00	1.75
2145	2482	9.956640	TGTGCCCTTTATTTAATTCATTCAAAT	57.043	25.926	0.00	0.00	0.00	2.32
2502	2983	6.123651	ACCAATTCTTGTTGTTACAGGTACA	58.876	36.000	0.00	0.00	35.28	2.90
2706	3220	9.180678	GTTATAACATTTTGAACACCTGTCTTG	57.819	33.333	10.81	0.00	0.00	3.02
2732	3264	4.451629	ACTTTATGGTGTACGAGTCCTG	57.548	45.455	0.00	0.00	0.00	3.86
2921	3473	9.825972	AATCTCTGTGTTTTATCATGTAAAACG	57.174	29.630	23.42	16.13	45.38	3.60
3032	3652	7.278868	CCTTCAGTTATCATCCTTGAACTGTAC	59.721	40.741	12.02	0.00	39.84	2.90
3142	3774	4.103785	CCCCACTCTACCAATCTCATGATT	59.896	45.833	0.00	0.00	43.10	2.57
3201	3839	4.320023	TGGTGTGAACGTGCAATATAACT	58.680	39.130	0.00	0.00	0.00	2.24
3456	4441	2.686915	AGTATCACTAACGAGGGTTCCG	59.313	50.000	0.00	0.00	37.58	4.30
3502	4489	5.753438	GGAAATGAAACCCAAAGAAGTGAAC	59.247	40.000	0.00	0.00	0.00	3.18
3866	5183	3.144285	CCATGGCGGTACCGGTAT	58.856	61.111	33.98	11.78	43.94	2.73
4055	5386	4.819630	AGTACGGAAAGAAGTTTGCATCAA	59.180	37.500	0.00	0.00	33.74	2.57
4446	5953	3.047807	GCTGTGCTGCCTGGGGATA	62.048	63.158	0.00	0.00	0.00	2.59
4554	6368	3.188048	GTCTTCCTGAAACATGACAGCTG	59.812	47.826	13.48	13.48	33.40	4.24
4555	6369	1.527034	TCCTGAAACATGACAGCTGC	58.473	50.000	15.27	7.45	33.40	5.25
4556	6370	1.072806	TCCTGAAACATGACAGCTGCT	59.927	47.619	15.27	0.00	33.40	4.24
4580	6394	5.691305	TCATTTTGCTGTTGTTATGCACTTC	59.309	36.000	0.00	0.00	36.37	3.01
4724	6726	5.298347	AGTTTCCGCAGTTTATATAGGCTC	58.702	41.667	0.00	0.00	0.00	4.70
4883	6887	2.113860	ATGTGATTACAGCAAGCCGT	57.886	45.000	0.00	0.00	40.79	5.68
4970	6974	2.621998	GGTGGTCTCGGAATCTCGATAA	59.378	50.000	0.00	0.00	38.55	1.75
5099	7116	4.096984	CCCTGTGTCTTTCCATATTCTTGC	59.903	45.833	0.00	0.00	0.00	4.01
5219	7241	8.327429	GGACCGTAAAATCAATGCATTTTATTG	58.673	33.333	9.83	0.00	39.35	1.90
5521	7623	5.417894	TCTGAGTAAGGAGTTTTGATCGCTA	59.582	40.000	0.00	0.00	0.00	4.26
5918	9123	4.096682	CCAACTACAACCGAAGTTCCAAAA	59.903	41.667	0.00	0.00	33.72	2.44
6049	9324	7.310609	CCATTAAAATCCATCCCACTTTCTGTT	60.311	37.037	0.00	0.00	0.00	3.16
6102	9377	6.160684	TGTGATTTCATTTCCAATCAGCAAG	58.839	36.000	0.00	0.00	39.53	4.01
6202	9528	4.922206	AGGCCACAAATTCAGATTACAGA	58.078	39.130	5.01	0.00	0.00	3.41
6289	9615	1.336125	GGCATCTACAATGCAAGAGCC	59.664	52.381	11.69	0.70	46.21	4.70
6343	9669	3.637911	ATTATGGAACTTGCGTGGGTA	57.362	42.857	0.00	0.00	0.00	3.69
6349	9675	2.093341	GGAACTTGCGTGGGTATAGGAA	60.093	50.000	0.00	0.00	0.00	3.36
6395	9721	4.623595	GCCTACTCAAGCGCTAATCTAATC	59.376	45.833	12.05	0.00	0.00	1.75
6396	9722	5.565834	GCCTACTCAAGCGCTAATCTAATCT	60.566	44.000	12.05	0.00	0.00	2.40
6557	9884	0.682209	CTTGAATCCTGGCACCTGGG	60.682	60.000	12.21	3.24	35.98	4.45
6629	9956	2.470990	ACTGAGTGGATGATGTAGCCA	58.529	47.619	0.00	0.00	44.07	4.75
6643	9970	9.440773	GATGATGTAGCCAACTATCATTATGAA	57.559	33.333	0.00	0.00	36.91	2.57
6797	10124	3.676172	TCAAAACACTTAGGCACGATACG	59.324	43.478	0.00	0.00	0.00	3.06
6873	10200	0.464373	ATGTGGGGCGTCTATGCTTG	60.464	55.000	0.00	0.00	34.52	4.01
7069	10398	8.918202	TTCCATAGTGGCCTTGTATAAATAAG	57.082	34.615	3.32	0.00	37.47	1.73
7174	10508	6.495181	TCAAATAATCCCAAAACACTTAGGCA	59.505	34.615	0.00	0.00	0.00	4.75
7189	10523	5.410439	CACTTAGGCACGGTACATTAACTTT	59.590	40.000	0.00	0.00	0.00	2.66
7280	10618	3.193479	TGAGACTATCAAGCACGACATGT	59.807	43.478	0.00	0.00	34.02	3.21
7382	10720	2.778299	GGTGCACAACCTAAGATGACA	58.222	47.619	20.43	0.00	46.55	3.58
7389	10727	6.539826	TGCACAACCTAAGATGACATATTCAG	59.460	38.462	0.00	0.00	37.77	3.02
7413	10751	3.396946	TGGACGGAGGGAGTACTATGTAT	59.603	47.826	0.00	0.00	0.00	2.29
7515	10860	3.054728	TGACAGGAGTTTGTTCCACTGAA	60.055	43.478	0.00	0.00	39.84	3.02
7540	10897	0.389025	TATGCCGTCGATCAGTGCAT	59.611	50.000	11.98	11.98	44.28	3.96
7669	11027	0.175989	CTCCCTTACTTGACTCGCCC	59.824	60.000	0.00	0.00	0.00	6.13
7780	11138	2.679059	CGACAAGATTGATGTGGGAGCT	60.679	50.000	0.00	0.00	0.00	4.09
7842	11214	3.973206	TCGCCTAAGAACTTCCAATCA	57.027	42.857	0.00	0.00	0.00	2.57
7845	11217	3.181506	CGCCTAAGAACTTCCAATCAAGC	60.182	47.826	0.00	0.00	0.00	4.01
7961	11422	6.096141	TGTGCTTCAGTCCAATAAAAGTTTGA	59.904	34.615	0.00	0.00	0.00	2.69
7980	11441	1.416401	GACAGTTGTGTCCTTCCCTGA	59.584	52.381	0.00	0.00	46.58	3.86
8003	11464	8.887264	TGAAAATAGAATTAGCAAGGGGTAAA	57.113	30.769	0.00	0.00	40.10	2.01
8015	11476	1.971481	GGGGTAAATTTATCCCGCGT	58.029	50.000	27.16	0.00	43.82	6.01
8072	11533	5.309020	TCTCTTGGAAGAAGGGATCCATATG	59.691	44.000	15.23	0.00	44.83	1.78
8073	11534	4.352001	TCTTGGAAGAAGGGATCCATATGG	59.648	45.833	16.25	16.25	44.83	2.74
8074	11535	2.988859	TGGAAGAAGGGATCCATATGGG	59.011	50.000	21.78	3.43	40.74	4.00
8076	11537	1.376649	AGAAGGGATCCATATGGGGC	58.623	55.000	21.78	13.22	37.22	5.80
8078	11539	1.005215	GAAGGGATCCATATGGGGCTG	59.995	57.143	21.78	0.00	37.22	4.85
8079	11540	0.103715	AGGGATCCATATGGGGCTGT	60.104	55.000	21.78	3.32	37.22	4.40
8080	11541	1.154216	AGGGATCCATATGGGGCTGTA	59.846	52.381	21.78	1.13	37.22	2.74
8193	11661	1.086696	CATTCGATCGGTTTGCCACT	58.913	50.000	16.41	0.00	34.09	4.00
8276	11749	6.693466	TGACAACTAACGACAGATTTGGATA	58.307	36.000	0.00	0.00	0.00	2.59
8277	11750	7.327975	TGACAACTAACGACAGATTTGGATAT	58.672	34.615	0.00	0.00	0.00	1.63
8278	11751	7.277760	TGACAACTAACGACAGATTTGGATATG	59.722	37.037	0.00	0.00	0.00	1.78
8279	11752	7.327975	ACAACTAACGACAGATTTGGATATGA	58.672	34.615	0.00	0.00	0.00	2.15
8280	11753	7.987458	ACAACTAACGACAGATTTGGATATGAT	59.013	33.333	0.00	0.00	0.00	2.45
8312	11785	2.564771	CATGTATTGGCACCATCGAGT	58.435	47.619	0.00	0.00	0.00	4.18
8727	12262	8.250332	AGATTTGTCAGTGTTACAAACAAACAT	58.750	29.630	17.84	10.62	46.40	2.71
8873	12408	4.080687	CACCGTTCCCCACCTAATTTTAA	58.919	43.478	0.00	0.00	0.00	1.52

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
112	113	4.522789	AGTTCTTGTTGACTTTTGTGTGGT	59.477	37.500	0.00	0.00	0.00	4.16
123	124	5.921408	ACTTATCTCACGAGTTCTTGTTGAC	59.079	40.000	0.00	0.00	0.00	3.18
171	173	8.973378	GTGATTTGCTACAGTAGAGAATGATAC	58.027	37.037	12.15	5.82	0.00	2.24
211	213	6.377996	TCAGAGGCATTTAGTATGCAATGTTT	59.622	34.615	11.39	0.00	46.21	2.83
293	296	6.533367	TGTACTGTTTTGGCAGATTGTTTTTC	59.467	34.615	0.00	0.00	39.62	2.29
296	299	5.590530	TGTACTGTTTTGGCAGATTGTTT	57.409	34.783	0.00	0.00	39.62	2.83
441	444	3.316868	TGCGAAATTTCCCGAGAAAAGTT	59.683	39.130	12.54	0.00	44.91	2.66
456	459	6.742718	CAGAAAGTTTATCGATGTTGCGAAAT	59.257	34.615	8.54	0.00	44.22	2.17
460	463	4.957971	ACAGAAAGTTTATCGATGTTGCG	58.042	39.130	8.54	0.00	0.00	4.85
569	575	8.506168	AGGATTTTCTTGCTGTTATTTCGATA	57.494	30.769	0.00	0.00	0.00	2.92
570	576	7.396540	AGGATTTTCTTGCTGTTATTTCGAT	57.603	32.000	0.00	0.00	0.00	3.59
573	579	9.691362	TTGTTAGGATTTTCTTGCTGTTATTTC	57.309	29.630	0.00	0.00	0.00	2.17
615	621	7.925993	TCGTCACATGATAAGTGTTTTTCTTT	58.074	30.769	0.00	0.00	38.16	2.52
653	659	6.920569	AATTATCGGTAACATCACTTGGAC	57.079	37.500	0.00	0.00	0.00	4.02
663	669	5.722263	TCGTCTCCAAAATTATCGGTAACA	58.278	37.500	0.00	0.00	0.00	2.41
676	682	1.724545	TCCCCTCTTTCGTCTCCAAA	58.275	50.000	0.00	0.00	0.00	3.28
715	722	6.500589	AGGAATATCCAAGCAACTAAGCTA	57.499	37.500	0.00	0.00	40.47	3.32
733	740	6.098266	GCACCCCAAGTTAATATTCAAGGAAT	59.902	38.462	0.00	0.00	36.20	3.01
766	773	1.545706	AAGACCCTGAGCTTCGGGAC	61.546	60.000	23.66	18.32	45.95	4.46
771	778	1.346068	AGTGACAAGACCCTGAGCTTC	59.654	52.381	0.00	0.00	0.00	3.86
777	784	4.223923	AGAATAAGGAGTGACAAGACCCTG	59.776	45.833	0.00	0.00	0.00	4.45
816	823	5.476091	TGAAGTTTTCAAGTTTTGGGTGT	57.524	34.783	0.00	0.00	36.59	4.16
903	911	3.211045	TCTTGCCTTTGACAGTACCAAC	58.789	45.455	0.00	0.00	0.00	3.77
919	927	6.867816	TGTGTGGAAACAATTATGAATCTTGC	59.132	34.615	0.00	0.00	46.06	4.01
948	956	7.360113	TGTGGAAATGATATGCTACAGTAGA	57.640	36.000	12.15	0.00	0.00	2.59
1094	1102	1.374125	CATGGCGTTGAGGTCACGA	60.374	57.895	0.00	0.00	0.00	4.35
1627	1953	1.020437	TTGCAACATGCTTCACACGA	58.980	45.000	0.00	0.00	45.31	4.35
1638	1964	5.707298	AGTTAACTAGACAGCATTGCAACAT	59.293	36.000	6.26	0.00	0.00	2.71
1741	2067	5.288712	CGCGTCAACAACTTATTGAGATAGT	59.711	40.000	0.00	0.00	39.30	2.12
1765	2091	8.219105	CCGTAGTTCTGTTGAAATTAACTGTAC	58.781	37.037	0.00	0.00	33.52	2.90
1778	2104	3.701532	TTTTTGCCCGTAGTTCTGTTG	57.298	42.857	0.00	0.00	0.00	3.33
1780	2106	2.556622	CCATTTTTGCCCGTAGTTCTGT	59.443	45.455	0.00	0.00	0.00	3.41
1866	2194	2.490509	GGGACGACATGTTTTAAAGGGG	59.509	50.000	0.00	0.00	0.00	4.79
1957	2293	0.240945	AATTTTGCCTGCGGTTCTCG	59.759	50.000	0.00	0.00	42.76	4.04
2359	2763	4.301628	CACAAAAGAGGAAAGCATGGAAC	58.698	43.478	0.00	0.00	0.00	3.62
2502	2983	2.497273	GGGACATAAAGGCAGCAACATT	59.503	45.455	0.00	0.00	0.00	2.71
2606	3087	7.333528	AGCAAACTACTTGAACAAAGAATGA	57.666	32.000	0.00	0.00	39.38	2.57
2679	3193	7.581476	AGACAGGTGTTCAAAATGTTATAACG	58.419	34.615	10.92	0.00	0.00	3.18
2706	3220	4.563061	ACTCGTACACCATAAAGTTGGAC	58.437	43.478	0.00	0.00	39.25	4.02
2732	3264	7.272948	CAGGACTCGTACAACATAAAGTTAGAC	59.727	40.741	0.00	0.00	38.74	2.59
3032	3652	7.621832	TTGTAGTTTGATTCGCTTCAATTTG	57.378	32.000	1.46	0.00	35.64	2.32
3266	4229	4.404073	AGCAGTCTAGCAAACTAGCAGTAT	59.596	41.667	0.00	0.00	44.83	2.12
3502	4489	5.400066	AGGTTGATAAAACAAAATCCCCG	57.600	39.130	0.00	0.00	0.00	5.73
3664	4981	7.322664	GCTATCCATTGAAAAATTTCACCTGA	58.677	34.615	8.04	5.71	45.99	3.86
3866	5183	5.337578	AGAAACAAACTTTTGGCAGCTAA	57.662	34.783	6.65	0.00	42.34	3.09
4055	5386	5.163540	GCTTGCTACATACACTACACCTACT	60.164	44.000	0.00	0.00	0.00	2.57
4187	5661	4.065789	GTCTACTTTTCACCCTTGACTGG	58.934	47.826	0.00	0.00	0.00	4.00
4554	6368	3.989167	TGCATAACAACAGCAAAATGAGC	59.011	39.130	0.00	0.00	34.97	4.26
4555	6369	5.224888	AGTGCATAACAACAGCAAAATGAG	58.775	37.500	0.00	0.00	40.35	2.90
4556	6370	5.199024	AGTGCATAACAACAGCAAAATGA	57.801	34.783	0.00	0.00	40.35	2.57
4746	6750	4.026640	CGCAAACTGGAATCACAACTTTTG	60.027	41.667	0.00	0.00	0.00	2.44
4923	6927	1.287815	CACTACCGCCGTCAGAACA	59.712	57.895	0.00	0.00	0.00	3.18
5125	7146	1.327303	GTTGGACCAAGTGGCATCAA	58.673	50.000	7.31	0.00	39.32	2.57
5219	7241	9.130312	CAGTTTTAGTACTCAGAAGTATGACAC	57.870	37.037	0.00	0.00	40.08	3.67
5521	7623	4.932200	CGAGACAGCTAAATCAACTTTCCT	59.068	41.667	0.00	0.00	0.00	3.36
5918	9123	2.868964	TTATAGGGCTGGAGGTCTGT	57.131	50.000	0.00	0.00	0.00	3.41
6049	9324	6.844097	ACTTTGAAGTAAGTTTGGTTTCCA	57.156	33.333	0.00	0.00	37.52	3.53
6161	9485	6.775629	GTGGCCTTGTATATAAAAATGGAGGA	59.224	38.462	3.32	0.00	0.00	3.71
6349	9675	1.146152	TCCTCCGTTGGGGAAACAAAT	59.854	47.619	0.00	0.00	46.61	2.32
6557	9884	3.668980	TACAACGCCGGGGCTTAGC	62.669	63.158	19.97	0.00	39.32	3.09
6564	9891	3.505184	GGCATGTACAACGCCGGG	61.505	66.667	20.26	0.00	35.79	5.73
6774	10101	4.150980	CGTATCGTGCCTAAGTGTTTTGAA	59.849	41.667	0.00	0.00	0.00	2.69
6797	10124	8.384607	AGAAAGAAGAAATGAGGTGAGTTAAC	57.615	34.615	0.00	0.00	0.00	2.01
6873	10200	3.260884	TGTTTGGTAGTCTCCAGTCATCC	59.739	47.826	0.00	0.00	38.80	3.51
7069	10398	7.448748	ACCAAAAACATAGTACTCCATTCAC	57.551	36.000	0.00	0.00	0.00	3.18
7174	10508	4.240096	CGAGGTGAAAGTTAATGTACCGT	58.760	43.478	0.00	0.00	33.55	4.83
7189	10523	6.285224	TGTCAAGAAATAAGAAACGAGGTGA	58.715	36.000	0.00	0.00	0.00	4.02
7270	10608	2.955614	ACTAACCACTACATGTCGTGC	58.044	47.619	21.76	0.00	0.00	5.34
7331	10669	3.181433	GGAGAAGGGGAAAACCAGAGAAA	60.181	47.826	0.00	0.00	42.91	2.52
7338	10676	1.147191	ACCAAGGAGAAGGGGAAAACC	59.853	52.381	0.00	0.00	39.11	3.27
7382	10720	2.700897	CTCCCTCCGTCCAACTGAATAT	59.299	50.000	0.00	0.00	0.00	1.28
7389	10727	2.134789	TAGTACTCCCTCCGTCCAAC	57.865	55.000	0.00	0.00	0.00	3.77
7515	10860	0.821517	TGATCGACGGCATACCTTGT	59.178	50.000	0.00	0.00	0.00	3.16
7540	10897	1.805428	GCGGCTTTTGGGCTTTCTGA	61.805	55.000	0.00	0.00	38.46	3.27
7669	11027	1.131883	GAATTGCTGCCAGTGCTAGTG	59.868	52.381	0.00	0.00	38.71	2.74
7728	11086	3.084039	TCATCTGCACCTTCACCATTTC	58.916	45.455	0.00	0.00	0.00	2.17
7780	11138	5.290493	TCACAAGGAAGTGAAAGAGCTAA	57.710	39.130	0.00	0.00	44.92	3.09
7842	11214	1.070601	GGCAACCAAACATCCTTGCTT	59.929	47.619	0.00	0.00	39.21	3.91
7961	11422	1.507140	TCAGGGAAGGACACAACTGT	58.493	50.000	0.00	0.00	0.00	3.55
7972	11433	7.201857	CCCTTGCTAATTCTATTTTCAGGGAAG	60.202	40.741	0.00	0.00	32.45	3.46
8003	11464	0.250597	GGGCCTTACGCGGGATAAAT	60.251	55.000	12.47	0.00	38.94	1.40
8015	11476	2.853430	TCCTGTATTTGGAGGGCCTTA	58.147	47.619	7.89	0.00	34.31	2.69
8072	11533	1.501582	AGAGGAAGATGTACAGCCCC	58.498	55.000	7.66	9.66	0.00	5.80
8073	11534	2.365941	GGTAGAGGAAGATGTACAGCCC	59.634	54.545	7.66	2.68	0.00	5.19
8074	11535	3.068873	CAGGTAGAGGAAGATGTACAGCC	59.931	52.174	7.66	3.21	0.00	4.85
8076	11537	5.886474	TGTACAGGTAGAGGAAGATGTACAG	59.114	44.000	10.91	0.00	44.67	2.74
8078	11539	6.773685	AGATGTACAGGTAGAGGAAGATGTAC	59.226	42.308	0.33	6.39	41.97	2.90
8079	11540	6.912426	AGATGTACAGGTAGAGGAAGATGTA	58.088	40.000	0.33	0.00	0.00	2.29
8080	11541	5.772004	AGATGTACAGGTAGAGGAAGATGT	58.228	41.667	0.33	0.00	0.00	3.06
8193	11661	4.373116	GCGAGGAGTCAACCGCCA	62.373	66.667	10.62	0.00	41.59	5.69
8312	11785	3.200605	TGCTTCCTCCATGAATCTGCTTA	59.799	43.478	0.00	0.00	0.00	3.09
8390	11865	1.340399	AAGGAGCGCCCATCTCATCA	61.340	55.000	15.92	0.00	37.41	3.07
8480	11955	1.899814	TCTCGATTAGTGTTGGTGGCT	59.100	47.619	0.00	0.00	0.00	4.75
8611	12146	9.167311	ACAAACTCATATTTCAGATACCAAGAC	57.833	33.333	0.00	0.00	0.00	3.01
8624	12159	8.766994	ATATACAAGGCCACAAACTCATATTT	57.233	30.769	5.01	0.00	0.00	1.40
8803	12338	5.424252	ACTGAAAATCGGTTATACTCCCTCA	59.576	40.000	0.00	0.00	30.35	3.86
8804	12339	5.915175	ACTGAAAATCGGTTATACTCCCTC	58.085	41.667	0.00	0.00	30.35	4.30
8894	12429	8.738106	TCAATTGCACATATGATTGTAGTTTGA	58.262	29.630	10.38	8.26	0.00	2.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.