genome.fa.s9.2.7.7.80.10.50.1000.83.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: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  70713020

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   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   

This is table  83  of  226  ( 27023 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)
29697233--29697279	25	1.9	25	82	4	60	53	6	10	29	1.60
29697391--29697434	19	2.1	20	84	16	54	61	4	0	34	1.16
29699454--29699487	14	2.4	14	85	0	50	67	5	2	23	1.26
29699498--29699536	11	3.5	11	83	13	53	64	17	12	5	1.46
29700418--29700474	16	3.5	16	75	17	55	75	1	17	5	1.07
29704813--29704879	32	2.1	32	100	0	134	28	14	5	50	1.66
29707794--29707872	40	2.0	40	85	5	106	15	29	17	37	1.90
29709222--29709259	16	2.5	15	83	8	51	68	0	0	31	0.90
29711865--29711915	5	10.2	5	100	0	102	39	19	0	41	1.52
29712661--29712734	28	2.4	31	76	17	82	32	22	22	21	1.98
29712666--29712731	28	2.4	28	87	2	89	30	22	24	22	1.99
29712861--29712940	26	3.1	26	88	0	115	36	21	22	20	1.95
29713074--29713220	27	5.5	27	83	8	160	21	19	20	38	1.93
29713090--29713205	53	2.2	53	84	4	153	22	16	23	37	1.93
29713104--29713220	27	4.4	27	84	11	161	20	19	19	40	1.92
29715571--29715595	5	5.0	5	100	0	50	80	0	0	20	0.72
29717273--29717310	19	2.0	20	89	5	60	39	0	2	57	1.12
29717589--29717640	26	2.0	27	84	3	70	28	1	1	67	1.12
29724324--29724360	9	4.3	9	80	13	51	35	0	0	64	0.94
29724625--29724668	21	2.1	21	83	8	54	38	2	2	56	1.24
29731271--29731299	13	2.2	13	100	0	58	27	24	17	31	1.97
29732225--29732262	20	1.9	20	84	10	51	50	5	5	39	1.48
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29738586--29738641	17	3.5	16	79	11	62	44	1	0	53	1.11
29739414--29739499	38	2.2	40	84	10	108	38	2	1	58	1.19
29739419--29739501	40	2.1	38	82	12	98	39	2	0	57	1.12
29741595--29741637	16	2.8	16	82	10	54	55	2	4	37	1.33
29742845--29742897	28	1.9	27	84	3	70	64	1	5	28	1.27
29742875--29742918	23	2.0	21	86	8	61	63	2	4	29	1.26
29742945--29743015	3	22.7	3	83	8	54	60	7	1	30	1.32
29743040--29743100	30	2.0	30	100	0	122	54	13	13	19	1.71
29746792--29746852	27	2.3	27	100	0	122	44	18	13	24	1.85
29746803--29746858	27	2.3	23	82	17	62	46	12	17	23	1.82
29749298--29749637	119	2.8	119	96	1	619	51	5	0	42	1.30
29749767--29749798	17	1.9	17	93	6	57	59	3	0	37	1.13
29750002--29750035	17	2.0	17	100	0	68	58	0	0	41	0.98
29749998--29750036	17	2.2	19	86	13	64	56	0	0	43	0.99
29749738--29750101	118	3.1	118	93	3	619	51	4	1	42	1.29
29751492--29751595	49	2.1	49	94	0	181	50	10	7	31	1.65
29754101--29754134	16	2.1	16	100	0	68	76	0	0	23	0.79
29754411--29754438	13	2.2	13	100	0	56	50	21	7	21	1.72
29755841--29755883	20	2.2	20	95	0	77	65	16	0	18	1.28
29762313--29762441	50	2.6	50	83	0	159	27	21	29	20	1.98
29763135--29763169	17	2.1	17	89	5	54	65	0	34	0	0.93
29763929--29763960	6	5.3	6	100	0	64	84	0	0	15	0.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29764050--29764089	2	20.0	2	100	0	80	0	0	50	50	1.00
29764618--29764745	45	3.2	38	76	15	123	17	22	22	36	1.95
29764645--29764790	45	3.2	45	86	0	193	17	18	22	41	1.91
29764777--29764816	6	6.3	6	88	2	53	17	17	17	47	1.83
29770699--29770748	24	2.1	24	85	7	66	50	6	2	42	1.38
29778119--29778181	4	15.8	4	86	0	90	46	25	4	23	1.72
29782253--29782328	23	3.3	23	94	0	125	28	26	19	25	1.99
29782554--29782592	18	2.2	17	86	13	53	46	20	0	33	1.51
29783747--29783778	2	16.0	2	100	0	64	50	0	0	50	1.00
29804663--29804753	30	3.0	30	93	0	146	17	28	15	38	1.90
29819757--29819791	10	3.4	10	92	7	61	25	2	8	62	1.38
29819788--29819826	17	2.2	18	86	4	53	41	0	0	58	0.98
29828109--29828139	2	15.5	2	100	0	62	51	0	0	48	1.00
29831643--29831689	19	2.6	18	71	18	51	48	17	0	34	1.47
29836747--29836875	63	2.0	63	93	0	222	35	14	13	36	1.85
29837242--29837266	12	2.1	12	100	0	50	32	0	16	52	1.44
29840307--29840401	31	3.1	31	70	10	86	45	1	16	36	1.55
29847336--29847384	24	2.0	24	96	0	89	28	18	12	40	1.86
29859769--29859823	20	2.8	19	86	10	83	40	9	0	50	1.34
29859771--29859831	21	2.8	22	75	25	67	39	9	0	50	1.35
29859795--29859831	15	2.4	16	86	13	60	37	10	0	51	1.37
29860566--29860611	16	2.9	15	87	6	56	50	0	6	43	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29860583--29860637	20	2.8	19	81	10	74	50	0	7	41	1.30
29863351--29863496	71	2.1	71	85	1	195	27	14	24	33	1.94
29871767--29871799	10	3.2	10	95	4	57	27	9	12	51	1.69
29872710--29872757	22	2.3	23	79	17	59	52	8	4	35	1.51
29872953--29873027	37	2.0	37	84	0	96	42	0	2	54	1.14
29873107--29873348	127	1.9	127	94	0	430	35	14	10	38	1.82
29877082--29877135	12	4.6	11	76	19	56	70	1	3	24	1.13
29878777--29878843	34	1.9	35	90	3	109	32	8	13	44	1.75
29879937--29879979	20	2.0	20	82	8	50	41	16	2	39	1.61
29885663--29885698	16	2.3	15	90	4	54	27	0	0	72	0.85
29886131--29886232	11	9.5	11	81	11	90	22	30	2	44	1.68
29886143--29886243	51	2.0	51	88	3	150	23	29	2	43	1.69
29886407--29886468	18	3.5	18	68	24	51	37	0	3	59	1.13
29887169--29887211	18	2.5	17	85	10	61	32	39	2	25	1.69
29888324--29888625	126	2.4	126	88	1	455	26	20	19	32	1.97
29888658--29888886	94	2.4	96	82	3	275	38	19	2	39	1.65
29892974--29893035	29	2.2	29	82	8	74	24	12	14	48	1.79
29918082--29918171	43	2.1	43	87	0	126	32	32	14	21	1.93
29918457--29918525	34	2.0	34	97	0	129	20	13	20	46	1.83
29918997--29919025	13	2.1	14	93	6	51	55	10	0	34	1.34
29923283--29923387	27	4.3	27	71	24	115	34	0	16	49	1.46
29923457--29923483	13	2.1	13	100	0	54	37	11	0	51	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
29925727--29925781	25	2.2	25	86	0	74	25	14	45	14	1.83
29937466--29937499	17	2.0	17	100	0	68	35	5	29	29	1.81
29937593--29937636	22	2.0	22	100	0	88	31	13	9	45	1.75
29939409--29939448	19	2.1	19	90	0	62	37	20	10	32	1.85
29940223--29940421	101	2.0	98	91	2	317	28	18	18	34	1.94
29953062--29953607	86	6.5	84	82	4	516	44	10	13	32	1.77
29954415--29954463	20	2.5	20	86	0	62	57	6	6	30	1.48
29960970--29961030	27	2.2	28	77	5	72	24	32	24	18	1.97
29967491--29967547	25	2.3	25	93	3	98	40	17	14	28	1.88
29972598--29972629	15	2.1	15	100	0	64	50	6	12	31	1.65
29973510--29973602	26	3.4	25	67	30	66	23	9	2	64	1.35
29973526--29973618	26	3.4	26	70	18	80	22	10	2	64	1.36
29976009--29976034	13	2.0	13	100	0	52	38	7	15	38	1.76
29978284--29978393	30	3.7	30	82	2	123	42	10	20	27	1.83
29980498--29980534	15	2.5	15	100	0	74	40	27	21	10	1.86
29981227--29981251	4	6.2	4	100	0	50	76	0	0	24	0.80
29992717--29992776	31	1.9	31	93	0	102	38	15	15	31	1.88
29992749--29993036	143	2.0	142	90	0	450	37	11	16	34	1.86
29993129--29993158	2	15.0	2	100	0	60	50	0	0	50	1.00
29999095--29999150	29	1.9	29	88	0	85	62	1	3	32	1.23
30000544--30000581	20	1.9	20	88	0	58	7	23	0	68	1.16
30000710--30000735	2	13.0	2	100	0	52	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)
30010949--30010975	2	13.5	2	100	0	54	48	0	0	51	1.00
30014956--30014982	11	2.5	11	100	0	54	48	18	0	33	1.49
30016117--30016170	23	2.3	23	96	3	99	40	14	18	25	1.89
30019312--30019364	23	2.2	26	86	10	76	56	0	5	37	1.23
30019300--30019389	23	4.0	23	72	20	64	53	0	10	36	1.35
30019381--30019430	22	2.3	22	80	13	59	62	2	4	32	1.25
30023754--30023796	19	2.1	21	87	8	63	60	2	2	34	1.22
30024640--30024685	17	2.6	17	86	3	56	32	0	6	60	1.22
30025135--30025201	31	2.2	31	83	0	80	25	5	10	58	1.54
30025156--30025214	31	1.9	31	86	3	84	23	10	10	55	1.63

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   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226