genome.fa.s5.2.7.7.80.10.50.1000.14.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: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  64140413

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   

This is table  14  of  208  ( 24913 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)
4296251--4296293	19	2.3	18	80	4	50	41	0	4	53	1.21
4312362--4312422	30	2.0	30	87	0	86	47	6	14	31	1.70
4314701--4315012	125	2.5	125	89	1	475	26	17	14	41	1.88
4314800--4315231	224	1.9	227	88	2	665	25	17	13	43	1.85
4314933--4315112	100	1.8	99	87	1	270	24	18	11	46	1.81
4315021--4315736	127	5.6	127	79	10	680	27	17	13	41	1.87
4315363--4315736	125	3.0	125	78	14	378	27	17	14	40	1.88
4327931--4327958	2	14.0	2	100	0	56	50	0	0	50	1.00
4328410--4328468	27	2.1	27	81	9	66	35	0	1	62	1.05
4334050--4334357	46	6.3	48	83	11	326	36	14	21	27	1.92
4334135--4334301	52	3.0	55	86	9	232	37	14	22	25	1.92
4334321--4334502	37	5.0	37	95	1	307	37	16	21	24	1.93
4337689--4337730	6	7.0	6	100	0	84	83	0	0	16	0.65
4345705--4345734	14	2.1	14	93	0	51	63	0	3	33	1.11
4346852--4346923	11	6.8	11	76	12	71	41	5	1	51	1.34
4346867--4346925	30	2.0	30	90	6	93	42	5	1	50	1.34
4346915--4346954	18	2.2	18	90	0	62	25	0	0	75	0.81
4346841--4346941	41	2.5	41	86	3	159	36	3	0	58	1.23
4346875--4346976	28	3.5	28	78	7	89	33	1	1	62	1.17
4349580--4349647	32	2.1	32	83	0	82	27	14	17	39	1.89
4353077--4353152	22	3.4	22	68	31	70	7	18	15	57	1.62
4353065--4353158	46	2.0	46	100	0	188	8	17	14	59	1.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4353080--4353154	24	3.2	24	69	30	72	8	17	17	57	1.63
4359864--4359891	3	9.3	3	100	0	56	35	0	32	32	1.58
4364346--4364378	5	6.6	5	92	0	57	3	0	54	42	1.15
4364625--4364681	29	2.0	28	83	13	71	35	1	7	56	1.37
4365940--4365973	9	3.8	9	84	0	50	50	2	0	47	1.16
4367379--4367405	4	6.8	4	100	0	54	48	25	0	25	1.52
4371944--4371997	21	2.5	20	77	11	54	61	16	11	11	1.57
4373166--4373214	11	4.4	11	76	5	53	38	2	0	59	1.09
4373177--4373232	23	2.4	23	80	17	62	35	0	3	60	1.14
4392033--4392098	32	2.2	28	76	19	71	33	12	25	28	1.92
4392041--4392109	32	2.2	32	91	0	111	33	13	24	28	1.93
4392086--4392111	11	2.4	11	100	0	52	30	19	23	26	1.98
4403282--4403324	18	2.4	18	88	7	61	48	0	0	51	1.00
4407920--4407963	21	2.1	21	83	8	54	38	0	4	56	1.20
4420552--4420682	58	2.3	58	81	5	156	28	16	15	39	1.89
4430724--4430895	83	2.1	83	97	0	326	34	22	11	31	1.89
4433013--4433079	22	3.0	22	77	16	75	41	19	20	17	1.90
4433016--4433080	23	2.9	22	77	11	69	41	18	20	20	1.91
4441567--4441610	19	2.3	19	84	7	54	25	4	4	65	1.30
4448769--4448798	7	4.4	7	91	8	53	40	0	60	0	0.97
4448769--4448798	13	2.2	13	94	5	51	40	0	60	0	0.97
4449602--4449661	3	20.0	3	96	0	111	31	0	1	66	1.01
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4456890--4456933	2	22.0	2	100	0	88	50	0	0	50	1.00
4460203--4460252	25	2.0	26	88	4	75	60	6	6	28	1.44
4460819--4460853	16	2.1	18	89	10	56	45	0	0	54	0.99
4461227--4461263	13	3.0	13	84	7	51	54	0	0	45	1.00
4461227--4461344	24	5.1	24	75	10	77	54	0	4	41	1.20
4461227--4461344	23	5.2	23	76	14	77	54	0	4	41	1.20
4461255--4461325	24	2.9	25	91	4	108	57	0	5	36	1.22
4461302--4461340	20	2.0	19	85	5	51	56	0	5	38	1.22
4464976--4465001	7	3.7	7	100	0	52	26	0	0	73	0.84
4467641--4467703	31	2.0	31	100	0	126	31	9	28	30	1.89
4468249--4468282	2	17.0	2	100	0	68	50	0	0	50	1.00
4468390--4468489	42	2.4	42	96	0	182	37	16	28	19	1.92
4470239--4470273	2	17.5	2	100	0	70	48	0	0	51	1.00
4473674--4473758	36	2.3	36	80	8	91	24	20	17	37	1.93
4479353--4479419	30	2.2	31	78	5	73	29	19	13	37	1.90
4480290--4480354	30	2.2	30	82	0	76	38	18	16	26	1.92
4481434--4481466	2	16.5	2	93	0	57	48	0	0	51	1.00
4484285--4484353	29	2.5	29	80	15	83	49	0	0	50	1.00
4484285--4484356	26	2.7	26	76	16	74	50	0	0	50	1.00
4484285--4484358	17	3.9	19	72	22	59	50	0	0	50	1.00
4488109--4488133	11	2.3	11	100	0	50	40	0	0	60	0.97
4496968--4497009	21	1.9	23	85	9	61	33	11	19	35	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4500685--4500717	11	3.3	10	88	12	50	57	0	42	0	0.98
4504951--4504996	2	23.0	2	100	0	92	50	0	0	50	1.00
4512856--4512881	13	2.0	13	100	0	52	7	7	7	76	1.15
4513409--4513571	82	2.0	84	90	2	258	22	20	25	30	1.98
4513420--4513572	40	3.8	40	82	7	191	24	22	24	28	1.99
4513667--4514501	44	19.0	45	67	14	256	24	23	24	27	2.00
4513667--4513886	45	4.9	45	75	9	200	23	23	22	30	1.99
4513668--4513886	89	2.5	89	89	0	312	23	23	22	30	1.99
4513668--4514673	88	11.5	88	87	2	1215	24	23	24	27	2.00
4514050--4514626	44	13.2	45	65	17	275	24	24	24	26	2.00
4515930--4515991	28	2.2	28	85	5	81	8	4	9	77	1.12
4523184--4523369	37	5.0	37	91	0	282	37	13	21	27	1.92
4523332--4523455	46	2.8	46	85	8	175	33	16	23	27	1.95
4524845--4524881	13	2.7	14	91	8	67	8	5	13	72	1.24
4525264--4525476	106	2.0	106	88	1	320	29	16	15	39	1.89
4528282--4528327	24	2.0	23	83	12	58	58	15	2	23	1.48
4529721--4529775	26	2.1	26	80	12	60	70	1	1	25	1.06
4534625--4534876	10	25.9	9	67	21	86	35	2	3	57	1.30
4534755--4534836	19	4.3	18	74	11	74	32	2	4	59	1.31
4534748--4534844	29	3.5	28	76	17	94	32	2	4	60	1.27
4535281--4535325	9	4.8	9	84	10	63	31	0	4	64	1.13
4535281--4535326	20	2.4	19	89	7	67	30	0	6	63	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4535295--4535332	20	1.9	20	88	0	58	31	5	7	55	1.51
4535339--4535395	27	2.2	26	78	6	62	36	3	0	59	1.14
4542035--4542112	24	3.3	24	76	7	97	28	12	11	47	1.76
4542023--4542114	46	2.0	46	97	0	175	30	11	11	45	1.77
4542023--4542097	22	3.3	22	72	7	78	30	12	12	45	1.77
4542944--4543002	31	1.9	31	92	0	100	22	22	3	52	1.61
4543096--4543157	22	2.8	22	95	0	106	33	19	29	17	1.95
4543140--4543193	25	2.2	25	86	6	74	38	20	24	16	1.92
4547833--4547912	41	2.0	41	92	0	133	27	21	20	31	1.98
4548167--4548220	12	4.2	12	74	21	56	42	9	5	42	1.60
4548281--4548312	2	16.0	2	100	0	64	50	0	0	50	1.00
4550776--4550834	31	1.9	31	92	0	100	22	22	3	52	1.61
4550926--4551052	25	5.3	24	81	10	129	40	21	22	15	1.91
4553452--4553501	24	2.1	24	96	0	91	42	4	22	32	1.72
4557186--4557349	43	3.9	42	76	15	167	31	29	18	21	1.97
4561498--4561545	24	2.0	24	95	0	87	43	4	22	29	1.72
4563449--4563485	17	2.2	17	90	0	56	83	2	5	8	0.88
4563733--4563790	22	2.7	21	79	10	64	51	0	6	41	1.28
4563729--4563781	24	2.2	24	86	3	72	50	0	9	39	1.35
4563959--4564014	29	1.9	29	86	13	80	19	8	10	60	1.55
4569217--4569261	21	2.0	22	84	16	58	42	11	0	46	1.39
4572349--4572406	28	2.1	28	90	0	89	48	15	0	36	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4576361--4576421	32	1.9	32	100	0	122	45	21	9	22	1.81
4576843--4576922	41	2.0	41	94	0	142	26	12	23	37	1.90
4578454--4578518	19	3.3	19	68	19	53	44	0	0	55	0.99
4579155--4579188	15	2.2	15	89	5	50	29	17	0	52	1.45
4585104--4585182	3	25.3	3	85	10	97	67	2	1	29	1.12
4587052--4587102	25	2.0	26	84	3	68	39	11	9	39	1.75
4588914--4588938	2	12.5	2	100	0	50	48	0	0	52	1.00
4588942--4588984	20	2.2	20	91	8	70	20	13	9	55	1.66
4589072--4589106	17	2.2	17	90	10	56	11	5	25	57	1.56
4594346--4594371	11	2.4	11	100	0	52	61	0	0	38	0.96

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