genome.fa.s11.2.7.7.80.10.50.1000.3.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.09

Please cite:
G. Benson,
"Tandem repeats finder: a program to analyze DNA sequences"
Nucleic Acid Research(1999)
Vol. 27, No. 2, pp. 573-580.

Sequence: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62681010

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190   191   192   
          193   194   195   196   197   198   199   200   201   202   203   204   205   206   207   208   
          209   210   

This is table  3  of  210  ( 25152 repeats found )

Click on indices to view alignment

Table Explanation

Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1003506--1003554	20	2.6	18	81	15	62	48	4	6	40	1.47
1003543--1003571	10	2.7	11	89	10	51	62	0	0	37	0.96
1011570--1011655	42	2.0	42	100	0	172	20	23	6	48	1.73
1014591--1014656	31	2.1	31	91	0	105	46	10	9	33	1.70
1024154--1024204	27	1.9	26	84	11	68	23	9	11	54	1.66
1033120--1033165	13	3.7	13	72	21	53	41	6	13	39	1.70
1037827--1037878	27	1.9	27	92	0	86	38	15	7	38	1.76
1037827--1037886	27	2.2	27	87	0	84	38	13	10	38	1.78
1038882--1039072	60	3.1	61	83	5	244	47	12	15	24	1.79
1042260--1042304	17	2.6	17	82	3	54	53	0	2	44	1.13
1055364--1055426	31	2.0	31	84	0	81	36	23	12	26	1.91
1055305--1055474	90	1.9	90	82	4	218	40	20	15	24	1.91
1062604--1062644	16	2.6	16	78	17	50	53	2	2	41	1.27
1064175--1064217	16	2.8	16	76	16	54	65	0	0	34	0.93
1064187--1064213	8	3.4	8	100	0	54	62	0	0	37	0.95
1065344--1065377	16	2.1	16	89	10	52	52	17	2	26	1.58
1066106--1066154	22	2.2	21	79	10	53	44	10	8	36	1.68
1067065--1067132	21	3.3	19	78	15	64	61	5	0	32	1.20
1067095--1067136	15	2.7	16	75	20	52	61	0	0	38	0.96
1069403--1069453	15	3.3	15	74	20	52	60	0	1	37	1.08
1069409--1069452	8	5.9	7	80	15	52	63	0	2	34	1.07
1069403--1069455	8	6.9	8	81	16	51	60	0	1	37	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1070547--1070594	25	2.0	24	83	4	60	72	10	0	16	1.10
1070870--1070900	2	15.5	2	100	0	62	48	0	0	51	1.00
1073188--1074232	75	14.0	75	82	5	1016	29	25	18	25	1.98
1075253--1075283	9	3.4	9	90	0	53	25	12	22	38	1.90
1075338--1075374	9	4.1	9	92	0	65	45	13	10	29	1.77
1084109--1084145	9	4.1	9	89	0	56	48	13	8	29	1.71
1084243--1084267	5	5.0	5	100	0	50	0	80	0	20	0.72
1100028--1100104	27	2.9	25	73	19	66	48	3	2	45	1.34
1108690--1108724	6	5.8	6	89	0	52	5	17	31	45	1.71
1117011--1117066	27	2.1	27	86	6	78	62	3	0	33	1.12
1117043--1117088	22	2.1	21	88	11	67	71	4	0	23	1.03
1126559--1126626	4	17.0	4	100	0	136	50	25	0	25	1.50
1127408--1127538	22	6.0	22	89	0	190	32	14	25	27	1.95
1127845--1127870	7	3.7	7	100	0	52	84	0	0	15	0.62
1129706--1129734	10	2.7	11	94	5	51	0	0	17	82	0.66
1135052--1135085	12	2.9	12	86	4	52	32	0	0	67	0.91
1135157--1135219	30	2.1	30	93	0	108	57	14	3	25	1.52
1137193--1137259	31	2.3	27	83	14	89	40	13	10	35	1.79
1144315--1144508	100	1.9	100	81	0	235	39	14	15	30	1.87
1155497--1155528	2	16.0	2	100	0	64	50	0	0	50	1.00
1156582--1156638	30	1.9	30	86	13	82	68	1	1	28	1.09
1159528--1159568	21	2.0	21	100	0	82	46	14	19	19	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1161757--1161811	29	1.9	29	92	3	94	56	12	3	27	1.53
1163372--1164136	228	3.4	229	87	1	1027	18	24	27	28	1.98
1176986--1177014	2	15.0	2	92	7	51	51	0	0	48	1.00
1179812--1179871	29	2.1	29	87	9	88	36	1	0	61	1.06
1179820--1179867	13	3.4	13	78	18	51	31	2	0	66	1.03
1182850--1182874	13	1.9	13	100	0	50	28	0	0	72	0.86
1188105--1188136	15	2.1	15	100	0	64	15	6	43	34	1.72
1192603--1192627	2	12.5	2	100	0	50	48	0	0	52	1.00
1193612--1193680	33	2.1	33	100	0	138	31	18	2	46	1.64
1194370--1194403	15	2.1	17	89	10	54	23	0	11	64	1.26
1198027--1198087	32	1.9	32	83	12	81	44	4	1	49	1.33
1200537--1200624	43	2.0	43	97	0	167	40	12	10	36	1.77
1202202--1202242	20	2.0	20	86	9	57	63	0	4	31	1.15
1202202--1202259	19	3.0	19	80	12	64	56	0	5	37	1.21
1215273--1215330	20	2.9	20	82	10	57	50	5	0	44	1.24
1219485--1219536	24	2.1	26	85	7	72	25	7	7	59	1.51
1224171--1224220	24	2.1	23	82	10	57	68	4	0	28	1.08
1224360--1224401	18	2.3	18	87	0	66	33	40	16	9	1.81
1224364--1224398	6	5.8	6	96	0	61	34	37	17	11	1.85
1226978--1227037	30	2.0	31	90	3	95	21	20	10	48	1.78
1227441--1227466	6	4.3	6	100	0	52	84	0	0	15	0.62
1227521--1227635	59	2.0	60	85	3	162	42	13	20	24	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1243774--1243798	12	2.1	12	100	0	50	24	36	24	16	1.94
1243959--1244012	9	5.9	9	81	12	65	40	29	9	20	1.83
1244156--1244185	13	2.3	13	94	0	51	16	3	40	40	1.65
1250867--1250908	18	2.2	20	83	8	52	57	9	0	33	1.31
1250935--1250960	13	2.0	13	100	0	52	69	0	7	23	1.14
1257862--1257898	16	2.4	16	86	8	51	2	10	10	75	1.14
1258932--1258972	2	20.5	2	89	0	64	46	2	2	48	1.28
1262531--1262573	18	2.3	19	84	8	52	41	0	4	53	1.21
1262489--1262664	80	2.2	80	86	3	248	40	3	3	51	1.39
1262607--1262670	17	3.6	17	78	14	76	40	0	1	57	1.08
1262623--1262673	26	1.9	27	84	4	68	39	0	3	56	1.18
1262737--1263015	70	3.9	70	75	10	260	41	4	2	50	1.36
1262942--1262980	17	2.3	17	90	0	60	48	0	2	48	1.15
1262982--1263021	20	2.0	21	85	5	55	37	5	0	57	1.21
1263442--1263493	15	3.4	15	72	15	52	40	0	0	59	0.97
1263436--1263507	31	2.4	30	86	4	92	34	0	2	62	1.10
1268503--1268587	43	2.0	43	90	0	134	43	2	4	49	1.36
1268526--1268589	9	7.3	9	75	16	55	42	1	3	53	1.26
1268613--1268648	18	2.0	18	88	0	54	50	0	0	50	1.00
1268638--1268674	17	2.2	17	90	0	56	56	0	2	40	1.13
1268708--1268755	17	2.7	18	83	6	53	56	4	0	39	1.19
1268646--1268792	79	1.9	80	91	1	242	50	4	4	41	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1272007--1272048	21	2.0	21	86	4	59	35	0	2	61	1.09
1272021--1272080	17	3.5	16	75	16	57	30	0	3	66	1.07
1277297--1277335	21	1.9	21	89	5	62	25	10	2	61	1.41
1279026--1279078	10	5.6	10	72	18	51	41	0	1	56	1.10
1279026--1279087	18	3.3	18	76	12	54	41	0	3	54	1.16
1279003--1279149	79	1.9	80	85	1	206	42	3	4	50	1.38
1279121--1279153	17	1.9	17	93	0	57	48	3	0	48	1.17
1283022--1283048	8	3.4	8	100	0	54	51	0	0	48	1.00
1283100--1283243	63	2.3	63	85	4	202	52	3	2	41	1.30
1283171--1283208	18	2.1	18	90	5	58	60	0	0	39	0.97
1283294--1283460	79	2.1	81	84	6	216	50	4	3	41	1.41
1283378--1283425	17	2.7	18	83	6	53	56	4	0	39	1.19
1286762--1286803	22	1.9	22	85	0	57	30	14	4	50	1.63
1290561--1290630	31	2.3	31	80	5	79	50	11	4	34	1.58
1301010--1301056	15	3.2	14	75	19	51	23	0	6	70	1.10
1301608--1301653	22	2.1	22	84	8	58	47	0	0	52	1.00
1301694--1301723	15	2.1	14	93	6	51	36	0	6	56	1.26
1303854--1303884	14	2.2	14	94	0	53	22	6	0	70	1.09
1314681--1314715	18	1.9	18	94	0	61	25	5	14	54	1.62
1315038--1315069	2	16.0	2	100	0	64	50	0	0	50	1.00
1318185--1318368	44	4.1	44	80	4	190	23	17	17	41	1.90
1318176--1318368	89	2.2	89	83	3	253	23	17	17	41	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1318348--1318403	6	9.2	6	80	3	67	17	19	14	48	1.81
1321415--1321605	50	3.8	50	89	0	283	25	24	30	19	1.98
1323831--1323939	56	1.9	56	94	0	191	33	15	21	30	1.94
1325078--1325108	4	7.8	4	100	0	62	25	0	22	51	1.48
1328433--1328540	21	5.1	21	83	5	110	34	24	24	17	1.96
1330153--1330274	23	5.3	23	96	0	226	30	28	21	19	1.98
1330500--1330538	18	2.2	17	86	13	53	46	20	0	33	1.51
1331376--1331466	36	2.5	36	82	10	105	30	19	1	48	1.56
1331516--1331555	16	2.5	16	88	11	64	25	25	0	50	1.50
1332621--1332659	21	1.9	20	84	5	51	41	7	2	48	1.45

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190   191   192   
          193   194   195   196   197   198   199   200   201   202   203   204   205   206   207   208   
          209   210