genome.fa.s9.2.7.7.80.10.50.1000.24.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  24  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)
10900514--10900568	2	27.5	2	100	0	110	50	0	0	49	1.00
10900680--10900718	8	4.9	8	81	12	53	61	0	2	35	1.10
10917158--10917182	12	2.1	12	100	0	50	20	16	0	64	1.30
10936898--10936946	25	1.9	26	95	4	91	34	16	14	34	1.89
10946496--10946529	13	2.7	13	86	4	52	38	5	14	41	1.70
10958749--10958786	5	7.6	5	100	0	76	42	39	0	18	1.50
10959957--10959985	2	14.5	2	100	0	58	51	0	0	48	1.00
10961527--10961567	21	2.0	21	90	0	64	43	17	17	21	1.87
10970744--10970829	39	2.2	39	89	4	138	56	1	1	40	1.14
10973824--10973887	21	3.0	22	90	4	103	0	32	15	51	1.44
10976169--10976393	60	3.8	59	95	3	398	54	0	8	36	1.31
10976169--10976392	29	7.5	30	95	3	391	54	0	8	36	1.31
10978108--10978167	11	5.4	11	74	9	59	36	3	0	60	1.14
10978100--10978170	33	2.2	33	100	0	142	33	2	0	63	1.09
10978132--10978208	40	1.9	40	100	0	154	32	2	0	64	1.07
10978190--10978228	20	2.0	20	89	0	60	38	2	0	58	1.12
10978189--10978246	20	2.8	20	80	17	57	41	1	3	53	1.28
10980352--10980386	19	1.9	18	88	11	54	57	0	5	37	1.23
10983113--10983145	15	2.2	15	100	0	66	27	0	0	72	0.85
10996799--10997040	3	80.7	3	72	4	112	9	24	30	36	1.86
10996799--10996977	42	4.4	42	81	6	190	7	22	31	37	1.83
10996790--10997008	42	5.4	39	74	8	141	8	23	30	38	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10996819--10997008	42	4.5	42	78	7	143	9	23	29	37	1.86
10996958--10997038	30	2.7	30	90	0	135	9	29	28	32	1.89
11006715--11006759	4	11.2	4	95	0	81	24	2	26	46	1.64
11010385--11010434	24	2.1	24	96	0	91	16	18	16	50	1.79
11017146--11017201	22	2.6	22	83	10	64	44	3	0	51	1.18
11017144--11017216	20	3.6	19	73	12	65	38	2	0	58	1.12
11017188--11017252	29	2.3	29	77	17	73	26	1	3	69	1.12
11032608--11032676	2	34.5	2	97	0	129	47	0	0	52	1.00
11034845--11034893	24	2.0	24	100	0	98	38	12	20	28	1.89
11063325--11063464	46	3.0	46	92	0	217	37	7	25	30	1.83
11069657--11069842	94	2.0	94	94	2	329	34	20	12	31	1.90
11073060--11073098	20	2.0	20	84	0	51	38	0	2	58	1.12
11077388--11077437	3	16.7	3	95	0	91	64	0	2	34	1.05
11077908--11078092	46	4.0	46	92	2	318	29	25	10	35	1.89
11079318--11079365	17	2.9	17	90	3	71	54	18	0	27	1.44
11080117--11081183	533	2.0	533	100	0	2134	38	19	10	32	1.85
11082192--11082444	46	5.6	46	93	2	433	28	23	15	32	1.95
11082192--11082444	91	2.8	91	95	1	447	28	23	15	32	1.95
11100052--11100076	4	6.2	4	100	0	50	48	0	0	52	1.00
11100441--11100476	2	18.0	2	100	0	72	50	0	0	50	1.00
11108440--11108506	3	22.3	3	100	0	134	67	0	0	32	0.91
11120863--11120921	28	2.0	31	84	12	81	54	1	1	42	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11120863--11120927	27	2.4	26	82	12	69	55	1	1	41	1.18
11120911--11120975	30	2.2	30	83	5	78	56	3	0	40	1.15
11120939--11121030	20	4.8	19	68	13	55	56	6	3	33	1.41
11121989--11122048	29	2.1	29	100	0	120	31	16	3	48	1.63
11122298--11122386	46	1.9	46	100	0	178	28	28	8	34	1.87
11123617--11123663	19	2.5	19	80	10	51	36	4	4	55	1.39
11123695--11123800	29	3.6	29	76	12	99	37	0	4	57	1.20
11123769--11123829	20	3.0	19	76	11	59	44	0	1	54	1.10
11131143--11131210	33	2.1	33	100	0	136	11	17	58	11	1.62
11132327--11132394	30	2.3	31	85	10	88	55	1	7	35	1.37
11135138--11135176	17	2.2	17	86	9	51	61	0	2	35	1.10
11144758--11144791	5	6.8	5	96	0	59	76	20	2	0	0.92
11149165--11149410	124	2.0	123	84	5	318	32	15	18	32	1.92
11163948--11163974	8	3.4	8	100	0	54	11	11	0	77	0.99
11167471--11167519	25	2.0	25	91	0	80	30	4	18	46	1.67
11177381--11177411	2	15.5	2	93	0	53	54	0	0	45	0.99
11183828--11183852	12	2.1	12	100	0	50	24	36	24	16	1.94
11184011--11184096	9	9.4	9	88	7	111	40	26	10	22	1.86
11185877--11185901	2	12.5	2	100	0	50	52	0	0	48	1.00
11186651--11186680	2	15.5	2	93	6	53	46	0	0	53	1.00
11190611--11190651	21	2.0	21	85	9	57	65	0	0	34	0.93
11191623--11191673	26	2.0	26	84	7	68	52	7	13	25	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11193022--11193053	2	16.0	2	100	0	64	50	0	0	50	1.00
11197244--11197297	17	3.1	17	70	19	56	46	14	12	25	1.81
11197227--11197297	36	2.0	36	97	0	133	46	12	12	28	1.78
11197229--11197289	17	3.5	17	72	16	61	47	11	13	27	1.77
11210580--11210628	25	2.0	24	88	4	71	61	0	0	38	0.96
11212913--11212946	15	2.3	15	90	10	52	32	0	2	64	1.08
11227959--11228027	31	2.2	31	86	0	93	49	5	2	42	1.41
11228247--11228308	22	2.7	24	82	9	76	48	1	1	48	1.21
11228284--11228323	16	2.5	16	91	0	62	47	2	7	42	1.45
11228312--11228454	68	2.1	67	92	2	243	40	4	9	44	1.59
11228396--11228423	9	3.1	9	100	0	56	32	0	10	57	1.33
11238890--11238926	14	2.6	15	79	12	51	62	0	0	37	0.96
11259717--11259771	24	2.3	24	93	0	92	16	29	18	36	1.92
11259717--11259799	24	3.4	26	83	9	86	15	25	19	39	1.91
11261264--11261402	46	3.0	46	85	2	181	30	23	10	36	1.87
11263513--11263549	17	2.2	17	95	0	65	24	2	21	51	1.61
11264090--11264201	46	2.4	46	93	0	197	32	8	30	28	1.88
11264549--11264642	46	2.0	46	87	0	134	30	26	8	34	1.86
11268169--11268228	29	2.1	29	87	6	88	25	0	6	68	1.14
11268266--11268323	20	2.9	20	73	14	57	46	5	1	46	1.35
11270699--11270750	26	2.0	25	82	10	61	59	9	1	28	1.40
11283110--11283182	27	2.6	29	83	10	82	39	23	6	30	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11292297--11292330	17	2.0	17	88	0	50	64	0	2	32	1.08
11293092--11293182	39	2.4	38	79	3	103	25	5	19	49	1.70
11303725--11303774	20	2.5	20	90	6	75	10	38	16	36	1.82
11303843--11303889	17	2.6	18	80	16	53	65	0	34	0	0.93
11303843--11303884	14	2.9	14	86	10	50	64	0	35	0	0.94
11304016--11304147	60	2.2	59	81	8	142	32	0	9	57	1.35
11304763--11304930	56	3.1	56	80	8	211	33	14	11	41	1.81
11305189--11305228	16	2.4	17	87	8	64	37	0	2	60	1.11
11309052--11309109	30	1.9	31	93	6	102	18	43	0	37	1.51
11309215--11309273	30	1.9	31	86	3	84	20	38	0	40	1.53
11309365--11309396	17	1.9	17	93	6	57	28	18	0	53	1.45
11310927--11310960	17	1.9	18	94	5	61	35	0	0	64	0.94
11327080--11327148	27	2.5	28	95	2	122	39	10	0	50	1.36
11327285--11327354	19	3.7	19	82	3	97	37	10	0	52	1.35
11327290--11327360	37	1.9	37	100	0	142	39	11	0	49	1.39
11327908--11327983	28	2.9	27	83	16	106	48	0	9	42	1.35
11327908--11328002	24	3.7	25	83	14	115	46	0	10	43	1.38
11327909--11328002	25	3.7	25	82	13	104	46	0	10	42	1.38
11329170--11329231	31	2.0	31	83	0	79	43	9	12	33	1.76
11342928--11342995	28	2.4	27	83	11	84	23	1	7	67	1.24
11343363--11343387	6	4.2	6	100	0	50	16	0	32	52	1.44
11343765--11343791	6	4.5	6	100	0	54	0	48	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11345364--11345421	3	19.3	3	89	0	80	58	0	6	34	1.25
11349637--11349695	29	2.0	29	96	0	109	25	23	6	44	1.78
11353365--11353535	95	1.8	94	86	6	249	38	24	13	23	1.91
11357913--11357959	24	2.0	24	95	0	85	36	12	31	19	1.89
11367747--11367787	21	2.0	21	85	0	55	29	21	4	43	1.73
11376009--11376048	4	10.0	4	94	0	71	25	2	25	47	1.64
11376793--11376832	18	2.2	18	86	8	55	52	5	2	40	1.37
11380336--11380395	26	2.3	26	80	11	61	36	23	21	18	1.95
11380815--11380853	5	7.6	5	82	5	51	43	17	2	35	1.63
11390790--11390846	26	2.1	27	83	3	71	17	19	35	28	1.94

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