genome.fa.s8.2.7.7.80.10.50.1000.185.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  185  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)
54931502--54931528	4	6.8	4	100	0	54	48	0	25	25	1.52
54931737--54931773	15	2.4	16	86	8	51	18	16	21	43	1.88
54937675--54937699	5	5.0	5	100	0	50	20	0	0	80	0.72
54938312--54938450	46	3.0	46	93	0	233	28	25	10	34	1.90
54941849--54941886	4	9.5	4	94	0	67	23	2	26	47	1.65
54953334--54953366	16	2.1	16	88	5	50	54	9	12	24	1.66
54954032--54954071	21	2.0	21	85	5	55	42	5	15	37	1.68
54954202--54954317	47	2.5	46	83	5	135	23	17	30	29	1.97
54954228--54954336	47	2.2	50	83	6	143	19	13	32	34	1.91
54954901--54955035	25	5.6	25	80	8	149	20	23	17	38	1.93
54960085--54960323	46	5.4	46	78	14	270	25	24	14	35	1.93
54960177--54960349	86	2.0	86	100	0	346	24	24	12	38	1.90
54970084--54970265	51	3.6	51	92	0	301	29	23	13	34	1.92
54982864--54982896	2	16.5	2	100	0	66	51	0	0	48	1.00
54988398--54988451	2	27.0	2	100	0	108	50	0	0	50	1.00
54998372--54998428	20	2.8	20	67	2	51	71	0	1	26	0.95
54998392--54998472	33	2.6	30	88	11	110	65	0	3	30	1.10
54998425--54998482	11	5.3	11	72	0	53	58	0	5	36	1.20
54998392--54998442	15	3.3	15	69	15	50	68	0	3	27	1.07
54998372--54998459	42	2.1	40	87	10	124	68	0	2	29	1.02
54998414--54998495	33	2.5	33	91	2	128	63	0	4	31	1.15
54999896--54999931	2	18.0	2	100	0	72	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55001269--55001545	46	6.0	46	96	0	491	28	28	9	33	1.87
55002777--55002818	17	2.6	16	88	7	66	52	21	0	26	1.47
55004040--55004073	17	1.9	18	88	5	52	44	20	2	32	1.67
55004599--55004700	37	2.6	38	74	10	100	30	26	21	21	1.98
55005257--55005281	7	3.6	7	100	0	50	60	0	0	40	0.97
55013604--55013654	10	5.0	10	83	4	66	70	9	9	9	1.34
55013604--55013648	21	2.2	20	88	4	63	71	8	8	11	1.32
55021678--55021710	2	16.5	2	93	0	57	51	3	0	45	1.16
55038533--55038589	26	2.2	26	83	0	69	59	3	8	28	1.44
55042974--55043002	4	7.5	4	92	7	51	48	0	0	51	1.00
55060638--55060672	2	17.5	2	100	0	70	51	0	0	48	1.00
55068505--55068600	31	3.2	30	71	14	81	25	10	13	51	1.73
55070657--55070708	18	2.7	20	74	17	56	59	0	3	36	1.16
55070798--55070837	20	2.0	20	90	0	62	50	10	10	30	1.69
55070786--55070852	34	1.9	35	87	3	100	46	11	8	32	1.72
55070821--55070860	14	2.9	14	84	0	53	42	15	7	35	1.75
55085895--55085936	21	1.9	23	90	9	70	52	2	2	42	1.27
55086332--55086395	29	2.2	30	82	2	76	42	1	7	48	1.41
55087193--55087254	25	2.5	26	78	7	65	45	3	1	50	1.27
55095078--55095103	2	13.0	2	100	0	52	50	0	0	50	1.00
55097624--55097676	16	3.4	16	81	2	72	52	1	16	28	1.54
55113536--55113569	13	2.5	14	90	9	61	35	23	5	35	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55118268--55118420	45	3.4	45	86	0	216	41	20	17	20	1.90
55128505--55128556	26	2.0	26	92	0	86	44	1	11	42	1.51
55128630--55128681	26	2.0	26	92	0	86	42	11	1	44	1.51
55138360--55138384	12	2.1	12	100	0	50	52	8	32	8	1.60
55146318--55146342	13	1.9	13	100	0	50	32	0	16	52	1.44
55166361--55166410	25	2.0	25	88	3	75	32	0	6	62	1.20
55167013--55167041	4	7.2	4	100	0	58	48	24	0	27	1.51
55186640--55186814	95	1.8	95	89	4	273	40	14	10	34	1.81
55189547--55189599	23	2.4	21	82	14	70	58	3	0	37	1.16
55189553--55189600	23	2.0	24	92	4	80	64	4	0	31	1.12
55194456--55194488	5	6.6	5	100	0	66	81	0	18	0	0.68
55201820--55201858	20	2.0	20	89	0	60	41	5	0	53	1.23
55203808--55203882	38	2.0	38	86	5	107	36	1	0	62	1.04
55203841--55203903	27	2.4	27	86	2	83	34	0	1	63	1.04
55205365--55205393	8	3.8	8	90	9	51	86	0	0	13	0.58
55205365--55205393	15	1.9	15	100	0	58	86	0	0	13	0.58
55207232--55207293	30	2.1	30	93	0	106	14	17	24	43	1.86
55210272--55210318	18	2.6	17	83	9	58	38	4	2	55	1.31
55211393--55211452	30	2.0	31	86	3	86	43	0	36	20	1.52
55225177--55225281	51	2.1	51	82	7	124	33	18	5	42	1.73
55228783--55228828	2	23.0	2	100	0	92	50	0	0	50	1.00
55232582--55232646	11	6.4	11	75	21	70	41	1	0	56	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55232565--55232658	38	2.4	39	82	5	129	39	1	0	59	1.04
55232629--55232668	21	1.9	21	84	0	53	40	2	0	57	1.12
55232531--55232661	70	1.9	69	82	9	160	38	1	0	60	1.06
55232820--55232859	11	3.8	10	83	9	53	57	2	0	40	1.12
55232818--55232859	21	2.0	22	85	4	59	57	2	0	40	1.12
55233061--55233089	2	14.5	2	100	0	58	51	0	0	48	1.00
55237287--55237319	2	16.5	2	100	0	66	51	0	0	48	1.00
55241076--55241136	10	5.8	10	71	9	50	49	1	0	49	1.10
55241074--55241142	32	2.2	32	81	5	77	46	4	0	49	1.21
55241085--55241170	32	2.9	32	81	15	112	43	3	0	53	1.18
55241085--55241188	32	3.5	29	84	11	106	43	2	0	53	1.15
55241148--55241188	19	2.1	20	90	4	66	39	2	0	58	1.11
55242241--55242294	18	2.9	18	77	2	54	40	42	1	14	1.57
55265732--55265776	23	2.0	22	82	4	54	53	0	4	42	1.21
55266794--55266830	16	2.2	16	85	4	56	62	16	0	21	1.33
55270791--55270928	10	13.0	10	66	14	62	53	2	2	40	1.31
55271434--55271486	29	2.0	25	85	14	70	33	0	1	64	1.05
55274085--55274123	18	2.2	18	86	9	53	25	23	10	41	1.86
55274530--55274595	24	2.7	24	95	4	114	33	0	3	63	1.10
55274531--55274687	24	6.7	23	71	14	99	35	0	3	60	1.17
55274470--55274687	117	1.9	117	92	1	366	35	2	3	58	1.28
55274510--55274747	54	4.2	54	73	15	169	39	0	3	55	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55274713--55274742	9	3.4	9	90	9	53	36	0	0	63	0.95
55278596--55278669	36	2.1	36	94	0	130	9	24	10	55	1.64
55281513--55281720	91	2.3	91	89	5	312	46	3	4	45	1.41
55281554--55281809	91	2.6	97	78	14	262	45	3	2	48	1.32
55281723--55281810	28	3.2	27	71	18	83	44	2	0	53	1.13
55281876--55281924	14	3.3	15	81	16	50	44	0	4	51	1.20
55285026--55285206	79	2.3	79	89	1	265	24	11	28	35	1.90
55286830--55286897	34	2.0	34	100	0	136	23	23	20	32	1.98
55289429--55289502	29	2.6	29	76	2	78	47	9	12	31	1.73
55300021--55300076	25	2.2	24	82	14	69	53	1	3	41	1.29
55300025--55300074	25	1.9	25	88	8	73	52	2	4	42	1.31
55313351--55313400	12	4.1	12	76	5	55	46	6	14	34	1.69
55313467--55313504	18	2.1	18	85	9	51	60	7	15	15	1.57
55314356--55314394	19	2.0	20	90	5	62	48	0	0	51	1.00
55316915--55316974	25	2.4	25	86	10	79	30	1	15	53	1.51
55341099--55341162	27	2.4	27	89	0	92	28	40	0	31	1.57
55349419--55349485	31	2.2	31	91	5	109	52	5	10	31	1.60
55349417--55349496	32	2.5	32	88	10	119	53	6	10	30	1.58
55349419--55349510	31	2.9	31	85	4	105	48	6	9	34	1.62
55350107--55350150	11	4.0	11	82	17	56	43	2	0	54	1.12
55356500--55356560	32	1.9	33	83	9	83	40	14	14	29	1.86
55365688--55365876	94	2.0	94	98	0	369	45	18	6	29	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55366465--55366503	3	12.7	3	89	5	60	64	0	2	33	1.08
55366656--55366699	23	2.0	23	86	4	63	40	2	4	52	1.34
55376492--55376557	31	2.1	30	83	10	80	33	15	13	37	1.86
55382230--55382288	26	2.2	27	84	3	75	37	1	0	61	1.07
55383329--55383387	31	1.9	31	83	13	77	25	20	11	42	1.86
55391849--55391907	31	1.9	31	85	0	82	37	13	8	40	1.75
55395752--55395786	4	8.8	4	100	0	70	22	0	0	77	0.78
55407848--55407874	13	2.1	13	100	0	54	40	7	0	51	1.30
55410871--55411041	85	2.0	86	97	1	326	48	16	15	19	1.81
55412595--55412628	17	2.0	17	88	0	50	23	2	2	70	1.15

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