genome.fa.s8.2.7.7.80.10.50.1000.4.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   

This is table  4  of  190  ( 22705 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)
1021917--1021968	19	2.9	18	72	16	54	26	13	13	46	1.80
1022766--1022797	16	2.0	16	100	0	64	37	0	37	25	1.56
1023017--1023266	119	2.1	119	94	0	437	52	6	0	41	1.32
1023958--1024078	40	3.0	40	100	0	242	50	7	14	27	1.70
1030197--1030229	2	16.5	2	100	0	66	51	48	0	0	1.00
1031692--1031734	22	2.0	22	90	0	68	55	6	30	6	1.53
1031694--1031741	22	2.2	22	81	3	62	58	6	25	10	1.54
1035271--1035314	17	2.8	15	77	12	52	59	2	0	38	1.10
1040416--1040467	3	17.3	3	100	0	104	34	0	0	65	0.93
1042818--1042844	5	5.4	5	100	0	54	0	18	0	81	0.69
1047346--1048066	357	2.0	357	96	0	1334	34	21	18	25	1.96
1055821--1055855	4	9.0	4	93	6	63	74	0	0	25	0.82
1056163--1056258	31	3.1	31	93	3	165	44	13	10	31	1.77
1058215--1058247	16	2.1	16	94	0	57	54	24	3	18	1.57
1064872--1064898	13	2.1	13	100	0	54	22	25	22	29	1.99
1069263--1069309	22	2.2	22	96	3	87	53	4	25	17	1.62
1075760--1075855	26	3.5	26	69	15	75	52	3	1	43	1.24
1075824--1075900	38	2.1	38	87	4	113	50	3	0	45	1.20
1077498--1077522	13	1.9	13	100	0	50	32	8	28	32	1.86
1078513--1078567	16	3.4	16	84	0	74	41	5	23	29	1.76
1078746--1078869	58	2.1	58	88	2	178	54	2	0	43	1.13
1081738--1081870	70	1.9	69	86	4	187	34	16	18	30	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1085346--1085398	13	4.1	13	85	0	79	28	7	28	35	1.84
1085568--1085629	30	2.1	29	82	11	72	46	0	4	48	1.23
1087907--1088156	123	2.0	123	99	0	491	30	29	16	24	1.96
1097199--1097224	2	13.0	2	100	0	52	50	0	0	50	1.00
1099443--1099550	54	2.0	54	94	0	189	45	12	12	29	1.79
1106308--1106338	12	2.5	12	94	5	53	29	29	19	22	1.98
1114929--1114990	30	2.0	31	93	3	108	27	6	22	43	1.77
1122753--1122817	30	2.2	30	86	5	87	50	6	1	41	1.36
1127011--1127060	25	2.0	25	88	0	73	34	16	10	40	1.81
1128826--1128889	2	32.0	2	87	0	92	43	50	6	0	1.27
1140465--1140546	31	2.8	29	73	10	85	53	9	10	25	1.66
1142432--1142976	114	4.8	112	75	10	444	30	17	24	26	1.97
1143079--1143114	18	2.0	18	89	10	56	25	0	5	69	1.10
1144062--1144137	7	11.0	7	83	8	84	10	0	43	46	1.38
1144062--1144136	27	2.7	27	91	2	114	9	0	44	46	1.35
1144061--1144111	20	2.5	20	93	3	84	7	0	50	41	1.31
1146453--1146488	16	2.2	16	95	0	63	27	11	8	52	1.65
1146965--1147011	13	3.7	12	86	11	58	42	10	2	44	1.51
1147675--1147898	9	25.4	9	70	13	146	46	20	2	30	1.63
1147717--1147899	25	7.1	25	69	17	90	46	20	1	30	1.60
1147648--1147828	98	1.8	99	81	5	224	46	19	2	30	1.62
1151279--1151322	22	2.0	22	90	0	70	45	27	18	9	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1153705--1153772	34	2.0	34	97	0	127	36	14	10	38	1.81
1157948--1158020	26	2.8	25	83	6	92	38	6	20	34	1.79
1164771--1164813	22	2.0	22	86	9	61	34	0	6	58	1.25
1171223--1171400	97	1.8	97	84	7	245	32	5	16	46	1.69
1172909--1172941	17	2.0	17	88	5	50	45	0	0	54	0.99
1173543--1173605	2	31.5	2	100	0	126	50	0	0	49	1.00
1175007--1175036	16	1.9	15	93	6	51	30	33	23	13	1.93
1175999--1176039	19	2.2	20	86	8	59	24	4	9	60	1.47
1178390--1178414	6	4.2	6	100	0	50	48	36	0	16	1.46
1182429--1182482	25	2.2	26	83	12	69	18	7	5	68	1.33
1184774--1184808	16	2.1	17	94	5	63	11	2	0	85	0.69
1184803--1184854	18	2.8	18	80	11	61	32	7	0	59	1.26
1184803--1184856	20	2.9	18	80	20	58	33	9	0	57	1.31
1186130--1186176	2	23.5	2	95	0	85	46	2	0	51	1.13
1186594--1186632	19	2.1	18	85	4	51	30	2	5	61	1.31
1187315--1187403	28	3.2	28	76	12	76	71	6	2	19	1.18
1187323--1187363	22	1.9	21	85	5	55	75	2	0	21	0.92
1187882--1187943	29	2.1	29	85	5	81	33	8	1	56	1.38
1190983--1191016	16	2.1	17	88	5	52	47	0	11	41	1.40
1192820--1192852	9	3.8	9	88	4	50	75	0	0	24	0.80
1214366--1214443	29	2.6	29	83	4	93	48	14	12	24	1.78
1214391--1214464	29	2.5	29	86	4	94	51	16	12	20	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1222181--1222227	8	5.4	9	78	17	55	65	0	2	31	1.04
1222181--1222248	17	4.3	15	78	15	66	69	0	2	27	1.03
1222466--1222649	60	3.2	59	78	6	187	42	15	19	22	1.89
1224171--1224203	18	1.9	17	88	11	50	54	0	0	45	0.99
1224471--1224501	16	1.9	16	93	0	53	45	0	0	54	0.99
1230757--1230893	57	2.3	57	82	8	159	27	20	27	24	1.99
1233912--1234024	47	2.4	47	78	8	115	37	14	21	27	1.92
1235770--1235812	23	1.9	22	85	4	59	39	0	0	60	0.97
1240358--1240429	22	3.3	22	94	0	117	25	27	16	30	1.97
1244460--1244704	96	2.6	95	88	3	368	38	19	1	40	1.62
1244812--1244909	40	2.5	40	84	0	133	24	24	23	27	2.00
1244812--1244920	40	2.7	40	80	2	130	24	22	22	29	1.99
1249408--1249459	24	2.2	24	83	13	63	53	9	3	32	1.51
1253123--1253167	19	2.3	20	78	17	51	35	2	2	60	1.22
1261088--1261113	2	13.0	2	100	0	52	50	0	0	50	1.00
1262066--1262121	20	2.7	21	80	5	69	32	0	5	62	1.18
1262196--1262230	18	1.9	18	88	0	52	31	5	11	51	1.61
1263776--1263831	24	2.2	26	84	9	80	50	0	3	46	1.19
1263776--1263833	25	2.3	24	80	16	73	50	0	3	46	1.18
1263817--1263847	13	2.4	13	94	0	53	61	0	3	35	1.12
1263776--1263840	24	2.6	25	77	20	73	49	0	3	47	1.17
1268862--1269125	72	3.6	73	79	7	304	39	11	12	36	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1273474--1273516	18	2.5	17	78	10	52	74	2	2	20	1.04
1273763--1273795	16	2.0	17	88	5	50	27	3	0	69	1.03
1285319--1285352	11	3.1	11	86	0	50	23	32	0	44	1.54
1285319--1285371	22	2.3	23	83	3	63	24	30	1	43	1.65
1286247--1286334	44	2.0	44	84	0	113	25	10	7	56	1.59
1289073--1289138	9	7.2	9	86	10	89	39	28	10	21	1.86
1289073--1289138	20	3.6	18	80	11	89	39	28	10	21	1.86
1289108--1289150	11	4.2	11	85	14	65	46	27	6	18	1.75
1290161--1290202	22	1.9	22	85	9	59	59	11	0	28	1.33
1290514--1290569	19	3.1	18	82	10	60	55	5	0	39	1.23
1290493--1290564	20	3.7	19	83	7	83	58	6	0	34	1.25
1291829--1291890	26	2.4	26	76	7	65	70	1	1	25	1.05
1294854--1294893	21	1.9	21	90	10	64	35	10	2	52	1.48
1297650--1297703	28	2.0	26	82	13	65	29	3	0	66	1.09
1297655--1297721	33	2.2	29	86	10	89	28	1	0	70	0.96
1298555--1298619	5	13.0	5	100	0	130	40	20	0	40	1.52
1314327--1314455	63	2.0	63	86	0	177	28	19	17	34	1.94
1314965--1314997	16	2.1	16	94	0	57	21	33	6	39	1.78
1339225--1339331	51	2.1	51	85	3	144	34	9	34	21	1.86
1351741--1351851	19	5.8	19	85	0	159	36	9	16	37	1.80
1353007--1353043	3	12.3	3	94	0	65	29	0	2	67	1.04
1353767--1353823	20	2.7	20	83	8	60	8	14	7	70	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1358869--1359074	103	2.0	103	86	0	286	33	8	20	36	1.83
1361076--1361100	3	8.3	3	100	0	50	0	32	0	68	0.90
1362334--1362380	2	23.5	2	95	0	85	48	0	51	0	1.00
1370764--1370805	16	2.6	16	92	0	66	42	7	2	47	1.43
1370779--1370833	22	2.5	22	84	0	74	43	1	1	52	1.22
1384674--1384713	20	2.0	20	90	0	62	25	0	2	72	0.97
1385906--1385943	20	1.9	20	88	0	58	21	13	15	50	1.78
1399521--1399550	2	15.5	2	93	6	53	46	0	0	53	1.00
1404127--1404187	30	2.0	30	90	0	95	40	18	14	26	1.89
1413911--1413945	2	17.0	2	94	5	61	48	0	2	48	1.16

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