genome.fa.s9.2.7.7.80.10.50.1000.222.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  222  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)
69402458--69402515	9	6.4	9	83	0	71	25	6	22	44	1.77
69402458--69402507	18	2.8	18	93	0	91	24	8	24	44	1.80
69402905--69402944	16	2.5	16	83	0	53	35	5	0	60	1.19
69414521--69414556	18	2.0	18	88	0	54	52	8	5	33	1.55
69414807--69414923	22	5.2	22	85	10	89	37	25	0	35	1.62
69414819--69414928	22	5.0	21	85	8	132	33	28	0	37	1.64
69414958--69415018	28	2.2	27	83	13	72	42	1	1	54	1.20
69414967--69415028	28	2.2	28	85	5	90	40	0	1	58	1.08
69415118--69415174	24	2.3	23	78	21	62	29	0	5	64	1.15
69419059--69419112	23	2.3	23	87	0	81	42	11	12	33	1.79
69423713--69423758	23	2.0	23	86	4	65	78	8	10	2	1.05
69425844--69425881	14	2.6	15	91	4	60	78	0	18	2	0.86
69426070--69426115	19	2.5	19	80	13	51	39	17	2	41	1.62
69427797--69427837	2	20.5	2	100	0	82	48	0	0	51	1.00
69432634--69432686	19	2.8	19	78	16	56	39	18	1	39	1.62
69434147--69434195	21	2.3	21	78	0	53	18	30	0	51	1.47
69435071--69435100	2	15.0	2	100	0	60	50	0	0	50	1.00
69437592--69437853	18	14.1	18	68	15	108	44	9	12	33	1.76
69437576--69437661	36	2.3	38	83	13	108	45	10	11	32	1.75
69437753--69437904	64	2.4	65	80	10	179	43	11	11	33	1.77
69437594--69437853	19	13.9	19	71	13	141	43	10	12	33	1.76
69437804--69437897	45	2.1	45	90	4	145	46	11	13	27	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
69437850--69437905	18	3.1	18	72	12	60	42	10	10	35	1.74
69437849--69437940	35	2.6	35	83	6	116	39	10	13	36	1.79
69437864--69437928	17	3.8	17	72	11	60	35	12	13	38	1.83
69437991--69438039	17	2.8	17	82	11	64	44	10	16	28	1.80
69438450--69438523	27	2.7	27	93	4	121	5	29	48	16	1.68
69438593--69438653	10	5.9	10	77	12	52	1	14	3	80	0.92
69438593--69438653	21	2.9	21	78	11	54	1	14	3	80	0.92
69438622--69438664	21	2.0	21	86	8	61	0	25	0	74	0.82
69438611--69438669	31	1.9	31	82	6	75	0	23	0	76	0.79
69439365--69439509	30	4.9	29	77	15	129	40	2	24	33	1.67
69439399--69439525	59	2.1	59	82	7	150	38	3	22	35	1.70
69439414--69439525	30	3.8	29	81	8	127	38	1	24	35	1.66
69439895--69439930	3	12.0	3	100	0	72	66	0	0	33	0.92
69440829--69440886	22	2.7	23	81	7	68	44	15	3	36	1.63
69440865--69440919	21	2.8	19	78	10	65	38	10	10	40	1.76
69441405--69441561	44	3.5	45	75	12	137	24	22	24	29	1.99
69441447--69441561	45	2.6	45	81	9	119	22	24	25	27	2.00
69441948--69442120	87	2.0	87	89	2	267	23	23	23	29	1.99
69441986--69442342	44	8.1	44	67	12	164	27	24	20	27	1.99
69442135--69442407	89	3.1	88	71	14	272	26	23	20	29	1.99
69443673--69443718	13	3.6	13	80	11	51	15	2	6	76	1.09
69443685--69443738	23	2.4	22	81	9	63	9	3	9	77	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
69449830--69449891	23	2.7	23	85	9	74	45	12	8	33	1.72
69450575--69450620	16	2.6	17	83	12	58	17	10	21	50	1.77
69450575--69450618	18	2.5	17	82	13	54	15	11	22	50	1.76
69453488--69453569	37	2.2	37	79	14	89	41	0	24	34	1.55
69466789--69466817	3	9.7	3	100	0	58	68	0	0	31	0.89
69467176--69467251	31	2.5	31	86	4	100	35	6	7	50	1.58
69467177--69467268	31	3.1	29	83	10	89	34	5	6	53	1.50
69469167--69469228	23	2.7	22	85	5	79	38	14	17	29	1.89
69475762--69475932	86	2.0	86	95	0	306	29	16	17	36	1.92
69477803--69477834	2	16.0	2	93	0	55	46	0	3	50	1.17
69481638--69481679	22	1.9	22	85	0	57	35	0	0	64	0.94
69485517--69485577	33	1.9	32	83	6	79	37	14	11	36	1.83
69488413--69488479	22	3.0	22	93	0	107	25	25	14	34	1.94
69497849--69497911	30	2.1	31	90	3	101	44	20	7	26	1.79
69497856--69497908	16	3.4	16	74	10	56	47	20	9	22	1.79
69497962--69497996	16	2.2	16	89	0	52	42	14	14	28	1.84
69499010--69499048	4	9.0	4	84	15	51	23	2	5	69	1.21
69511271--69511295	12	2.1	12	100	0	50	36	24	16	24	1.94
69512060--69512091	16	2.0	16	100	0	64	50	12	0	37	1.41
69514517--69514580	22	2.9	22	77	6	67	25	10	26	37	1.89
69514421--69514616	104	1.9	102	90	2	311	32	15	21	31	1.94
69516072--69516201	63	2.1	63	98	0	251	23	40	11	24	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
69518099--69518149	4	12.8	4	100	0	102	50	23	0	25	1.49
69518387--69518445	29	2.0	30	86	3	84	22	23	15	38	1.92
69518391--69518454	29	2.2	27	76	15	65	20	26	15	37	1.92
69521401--69521466	33	2.0	33	84	0	87	36	12	6	45	1.66
69522211--69522254	18	2.4	20	75	21	51	29	0	4	65	1.12
69527186--69527699	161	3.2	159	86	5	641	23	17	19	39	1.92
69527563--69527834	139	1.9	139	87	2	393	25	18	18	37	1.93
69527713--69528281	155	3.6	156	84	6	702	22	16	21	39	1.92
69529800--69529930	62	2.1	63	84	10	173	44	9	4	41	1.57
69537334--69537388	22	2.5	22	100	0	110	47	20	7	25	1.75
69541313--69541538	89	2.6	87	82	3	247	34	18	7	39	1.78
69541380--69541573	88	2.2	88	87	7	295	35	19	8	36	1.82
69541602--69541646	20	2.3	20	84	3	65	64	0	2	33	1.06
69541676--69541731	28	2.0	28	83	10	71	64	3	3	28	1.27
69541853--69542026	92	1.9	92	92	2	298	29	11	22	36	1.89
69542363--69542434	27	2.4	30	76	13	78	34	0	4	61	1.16
69542815--69542842	2	14.0	2	100	0	56	50	0	0	50	1.00
69544029--69544145	9	12.2	10	69	13	68	39	4	0	56	1.19
69543991--69544103	27	4.1	28	74	5	86	33	6	1	58	1.33
69543991--69544134	28	5.1	27	70	11	76	34	6	1	57	1.32
69544031--69544123	19	5.1	17	76	14	53	39	5	0	54	1.23
69544078--69544125	19	2.5	19	100	0	96	41	8	0	50	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
69544209--69544431	89	2.5	89	81	5	232	30	6	23	38	1.81
69545655--69545726	33	2.2	33	85	9	94	83	1	12	2	0.82
69545659--69545729	21	3.1	23	82	11	83	83	1	11	4	0.86
69545655--69545726	11	6.5	11	76	12	76	83	1	12	2	0.82
69555904--69556095	88	2.2	87	87	5	289	36	19	9	34	1.84
69556124--69556168	20	2.3	20	84	3	65	64	0	2	33	1.06
69556533--69556582	9	5.3	9	88	9	73	40	0	0	60	0.97
69556496--69556582	9	9.4	9	75	17	63	37	1	0	60	1.04
69556650--69556825	92	1.9	92	89	2	273	28	10	22	38	1.87
69556650--69556867	92	2.4	92	83	6	257	30	9	22	38	1.86
69558534--69558589	29	1.9	29	92	0	94	37	1	23	37	1.65
69561464--69561684	72	3.1	71	90	2	318	30	22	19	27	1.98
69566278--69566343	24	2.7	25	88	9	100	33	6	4	56	1.44
69566467--69566537	16	4.3	15	71	16	52	40	2	1	54	1.23
69566483--69566523	15	2.4	19	84	15	54	41	4	0	53	1.22
69567483--69567508	3	8.7	3	100	0	52	69	30	0	0	0.89
69568923--69568961	21	1.9	20	84	5	51	41	0	0	58	0.98
69572602--69572706	55	1.9	55	82	0	129	42	17	9	30	1.81
69578348--69578405	26	2.2	26	82	11	66	34	0	3	62	1.12
69586724--69586748	11	2.3	11	100	0	50	88	0	12	0	0.53
69588337--69588373	17	2.2	17	100	0	74	40	13	21	24	1.89
69589407--69589541	67	2.0	67	95	0	243	27	33	18	20	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
69589615--69589753	57	2.3	60	84	11	180	23	25	20	31	1.98
69593388--69593417	12	2.5	12	94	0	51	33	3	0	63	1.11
69593797--69594063	131	2.0	131	91	1	437	38	12	12	36	1.81
69596410--69596479	35	2.0	35	100	0	140	37	11	11	40	1.77
69597162--69597188	14	1.9	14	100	0	54	66	0	0	33	0.92
69598183--69598221	20	2.0	20	84	0	51	33	2	0	64	1.08
69602827--69602872	3	15.3	3	88	0	65	34	4	0	60	1.16
69603215--69603284	35	1.9	36	86	11	99	34	12	2	50	1.56
69603819--69603843	12	2.1	12	100	0	50	24	8	32	36	1.84
69604128--69604161	18	1.9	17	94	5	59	38	8	0	52	1.33

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