genome.fa.s7.2.7.7.80.10.50.1000.3.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: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  60982465

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   

This is table  3  of  204  ( 24458 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)
1023195--1023259	30	2.2	29	83	5	85	13	15	6	64	1.47
1027439--1027495	28	2.0	28	83	10	71	42	10	10	36	1.74
1037668--1037722	26	2.1	26	80	12	60	49	9	0	41	1.34
1044653--1044710	25	2.3	25	87	0	89	41	18	20	18	1.91
1052201--1052402	48	4.2	48	85	6	246	37	19	21	22	1.95
1052201--1052402	97	2.1	97	84	5	257	37	19	21	22	1.95
1055325--1055431	33	3.2	33	85	0	133	14	14	46	24	1.82
1055583--1055641	21	2.7	21	76	5	64	30	8	1	59	1.37
1055725--1055760	13	2.8	13	84	16	56	30	5	0	63	1.17
1055987--1056080	11	8.8	11	74	14	81	18	20	0	61	1.34
1055988--1056080	16	5.9	16	80	7	93	18	20	0	61	1.35
1055988--1056080	5	17.6	5	82	10	89	18	20	0	61	1.35
1056170--1056249	26	3.0	26	66	10	72	28	11	1	58	1.40
1056170--1056267	53	1.9	50	84	10	128	27	12	1	59	1.40
1059097--1059266	51	3.6	47	76	10	166	24	27	21	27	1.99
1061620--1061945	50	6.6	49	80	8	333	23	23	20	32	1.98
1061631--1061945	99	3.2	97	78	9	343	23	23	20	32	1.98
1061658--1061945	148	1.9	148	84	5	386	22	22	21	32	1.98
1061620--1061945	98	3.3	98	79	8	313	23	23	20	32	1.98
1079086--1079138	2	26.5	2	100	0	106	50	0	0	49	1.00
1080013--1080057	16	2.8	17	80	10	58	62	6	2	28	1.33
1082566--1082617	20	2.7	21	74	17	58	61	0	3	34	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1082566--1082616	18	2.7	19	72	6	50	60	0	3	35	1.15
1082630--1082715	33	2.6	33	77	1	93	48	18	6	25	1.73
1082691--1082767	14	5.0	15	70	20	52	45	14	6	33	1.70
1083529--1083598	31	2.3	31	78	12	72	38	22	10	28	1.87
1086093--1086199	54	2.0	53	96	1	196	23	14	14	47	1.81
1086801--1087008	113	1.8	113	89	4	330	22	25	27	23	2.00
1088162--1088263	39	2.7	38	74	6	98	37	1	15	45	1.58
1090031--1090056	12	2.2	12	100	0	52	30	7	0	61	1.24
1097726--1097783	27	2.2	27	93	3	100	12	24	10	53	1.68
1100786--1100840	28	1.9	29	85	3	76	45	1	0	52	1.11
1100786--1100847	28	2.1	29	82	5	72	43	3	0	53	1.17
1107145--1107183	20	2.0	20	94	0	69	30	30	12	25	1.93
1123659--1124339	236	2.9	231	83	5	768	40	20	16	22	1.91
1134362--1134391	12	2.6	11	90	10	51	53	0	3	43	1.17
1135445--1135491	18	2.7	19	81	15	57	63	0	0	36	0.94
1135451--1135488	15	2.4	17	82	8	53	63	0	0	36	0.95
1140530--1140693	43	3.9	43	78	4	163	29	15	25	29	1.96
1145240--1145289	24	2.1	24	85	14	68	62	0	0	38	0.96
1145365--1145420	29	2.0	28	85	3	76	23	10	14	51	1.73
1145639--1145687	11	4.4	11	92	2	71	20	32	2	44	1.63
1145639--1145698	22	2.7	23	84	7	79	21	30	1	46	1.61
1151095--1151137	14	3.0	15	80	10	54	34	6	16	41	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1151118--1151157	20	2.0	20	90	0	62	27	10	12	50	1.72
1152099--1152163	31	2.0	32	88	5	96	36	3	46	13	1.60
1155927--1155967	18	2.3	18	91	0	64	29	19	31	19	1.96
1155935--1155976	18	2.3	18	91	0	66	28	14	33	23	1.94
1155963--1156057	24	4.0	24	73	0	64	23	16	40	20	1.91
1161105--1161134	4	7.5	4	100	0	60	76	0	0	23	0.78
1164380--1164420	18	2.3	18	86	0	55	29	17	34	19	1.94
1164388--1164450	18	3.5	18	76	8	56	26	14	41	17	1.88
1174718--1174757	4	10.0	4	84	10	55	0	25	0	75	0.81
1179288--1179327	2	20.0	2	100	0	80	50	0	0	50	1.00
1181006--1181041	2	18.0	2	100	0	72	50	0	0	50	1.00
1183664--1183700	16	2.3	16	100	0	74	24	8	35	32	1.85
1185330--1185362	16	2.1	16	94	0	57	24	27	0	48	1.51
1190304--1190365	31	1.9	32	87	6	90	46	11	8	33	1.69
1195047--1195110	21	3.2	20	78	10	69	73	3	1	21	1.06
1195047--1195113	9	7.0	9	71	18	55	71	2	1	23	1.08
1199832--1199869	17	2.2	18	86	13	53	76	0	21	2	0.91
1206379--1206444	29	2.3	28	80	17	73	43	4	9	42	1.56
1214121--1214184	24	2.7	23	76	11	67	67	0	32	0	0.91
1214946--1214989	22	2.0	21	83	12	54	65	15	0	18	1.27
1221780--1221814	2	18.0	2	94	5	63	48	0	0	51	1.00
1222543--1222585	22	2.0	22	100	0	86	23	25	13	37	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1229009--1229052	19	2.2	20	80	4	54	50	2	4	43	1.35
1253352--1253394	19	2.3	19	80	19	54	23	11	0	65	1.25
1275794--1275833	2	20.0	2	94	0	71	50	2	0	47	1.14
1280432--1280467	16	2.2	16	100	0	72	52	0	0	47	1.00
1296716--1296775	19	3.2	19	72	11	52	55	1	0	43	1.10
1296772--1296812	18	2.3	18	91	0	64	73	2	2	21	1.07
1296761--1296934	56	3.1	55	75	11	133	59	1	6	32	1.32
1296826--1296878	27	2.0	27	81	7	63	64	1	5	28	1.27
1296783--1296924	55	2.5	58	78	12	152	61	2	6	30	1.32
1296787--1296909	65	1.9	65	80	6	142	59	2	5	32	1.34
1296874--1296918	21	2.1	21	84	8	56	57	2	11	28	1.45
1297361--1297550	91	2.1	91	89	3	285	28	8	21	42	1.82
1301160--1301211	19	2.7	21	77	16	60	32	7	1	57	1.38
1309749--1309778	15	2.0	15	100	0	60	6	33	13	46	1.69
1320869--1320894	12	2.2	12	100	0	52	53	7	30	7	1.57
1331168--1331212	19	2.5	19	85	7	58	35	2	2	60	1.22
1336994--1337054	30	2.0	31	93	6	106	32	0	0	67	0.91
1337011--1337064	25	2.2	25	93	0	90	29	0	0	70	0.88
1337011--1337074	25	2.6	25	85	9	78	26	0	3	70	1.02
1339978--1340027	14	3.6	14	74	15	50	68	14	8	10	1.40
1340698--1340736	18	2.2	17	95	4	69	28	2	10	58	1.44
1340798--1340830	9	3.7	9	84	15	50	27	9	18	45	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1344484--1344533	22	2.3	22	92	0	82	36	16	20	28	1.93
1358265--1358326	15	4.3	15	78	10	58	67	1	0	30	1.00
1360063--1360111	27	1.9	25	84	12	64	67	14	4	14	1.37
1364270--1364314	15	2.9	16	79	20	51	60	0	0	40	0.97
1367955--1368047	44	2.1	43	98	2	177	21	12	17	48	1.80
1373713--1373762	18	2.8	17	79	11	55	34	10	4	52	1.54
1387252--1387310	24	2.5	24	78	10	75	30	22	27	20	1.98
1387392--1387518	24	5.3	24	81	3	139	26	22	37	13	1.91
1387390--1387518	48	2.7	48	92	0	213	27	21	37	13	1.90
1387582--1387661	24	3.3	24	75	6	81	30	25	28	16	1.96
1387743--1387952	24	8.8	24	82	0	240	28	23	34	13	1.93
1387743--1387952	48	4.4	48	87	0	276	28	23	34	13	1.93
1390187--1390264	16	4.8	17	77	13	83	43	3	3	48	1.39
1394517--1394541	2	12.5	2	100	0	50	48	0	0	52	1.00
1399658--1399688	2	15.5	2	93	0	53	51	0	0	48	1.00
1402237--1402271	15	2.4	14	95	4	61	20	0	2	77	0.90
1403016--1403065	2	25.5	2	95	4	93	50	0	0	50	1.00
1403333--1403375	21	2.0	21	86	0	59	30	2	2	65	1.18
1407424--1407456	2	16.5	2	100	0	66	48	0	0	51	1.00
1409812--1409837	13	2.0	13	100	0	52	46	15	7	30	1.74
1410720--1410779	23	2.5	25	81	10	79	30	40	25	5	1.77
1410865--1410918	7	7.3	7	82	14	56	81	0	18	0	0.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
1410864--1410917	16	3.5	16	87	7	85	81	0	18	0	0.69
1410875--1410918	21	2.1	21	91	0	70	81	0	18	0	0.68
1410861--1410915	8	7.0	8	76	19	62	81	0	18	0	0.68
1411040--1411100	32	1.9	32	83	6	79	21	4	11	62	1.47
1411321--1411480	17	8.4	19	70	17	93	34	11	8	45	1.71
1411338--1411389	21	2.5	21	87	0	77	42	9	5	42	1.61
1411379--1411463	35	2.3	37	82	15	106	34	10	8	47	1.68
1411453--1411489	19	1.9	20	88	5	58	32	16	10	40	1.83
1417397--1417440	23	2.0	22	90	4	70	45	4	6	43	1.51
1420359--1420419	30	2.0	30	100	0	122	57	6	6	29	1.49

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