genome.fa.s4.2.7.7.80.10.50.1000.140.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: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

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   

This is table  140  of  198  ( 23681 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)
44593155--44593321	72	2.3	72	85	3	230	55	11	6	25	1.60
44593746--44593811	18	3.7	18	95	0	114	37	12	15	34	1.84
44599597--44599657	7	8.7	7	78	7	61	37	0	3	59	1.14
44599592--44599664	35	2.1	35	100	0	146	32	0	5	61	1.19
44599688--44599832	21	7.1	21	72	13	124	28	0	15	56	1.39
44599643--44599835	101	1.9	101	88	4	291	29	0	15	55	1.41
44599688--44599835	40	3.7	40	67	20	110	28	0	15	56	1.40
44599802--44599886	27	3.0	29	89	6	147	29	0	14	56	1.38
44599697--44599886	48	3.7	49	69	24	140	30	0	14	55	1.40
44599879--44599999	59	2.0	60	87	4	174	32	0	14	52	1.47
44600117--44600151	16	2.3	15	90	5	52	31	5	5	57	1.46
44601944--44601972	14	2.0	15	93	6	51	58	0	0	41	0.98
44601992--44602029	18	2.1	19	90	5	60	47	0	2	50	1.15
44610115--44610151	2	18.5	2	100	0	74	51	0	0	48	1.00
44611100--44611148	19	2.6	19	75	12	55	10	12	8	69	1.37
44613243--44613290	15	3.1	15	88	11	78	37	0	6	56	1.25
44613243--44613288	17	2.8	17	93	6	78	36	0	6	56	1.25
44613330--44613364	17	2.1	17	100	0	70	34	0	0	65	0.93
44613433--44613483	18	2.9	18	85	8	61	39	1	0	58	1.09
44613459--44613510	16	3.5	15	80	17	56	36	1	0	61	1.07
44613454--44613495	16	2.5	18	77	18	54	40	2	0	57	1.12
44613470--44613525	28	2.0	29	86	10	80	39	0	1	58	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44613568--44613721	18	8.9	18	66	18	76	42	0	2	54	1.19
44613266--44613863	122	5.0	120	93	2	1017	42	1	4	52	1.28
44613266--44613872	242	2.5	238	93	2	1013	42	0	4	52	1.28
44614008--44614097	45	2.0	45	91	6	148	37	27	4	30	1.76
44614076--44614113	16	2.4	16	90	0	58	26	31	2	39	1.70
44626352--44626404	21	2.4	21	78	6	52	35	5	1	56	1.34
44630367--44630427	26	2.3	26	91	5	97	44	22	0	32	1.54
44630830--44630911	36	2.3	36	85	6	114	36	25	7	30	1.83
44634967--44635004	17	2.2	17	95	0	67	44	5	21	28	1.73
44640659--44641247	131	4.5	131	91	0	919	30	20	25	23	1.99
44645252--44645298	22	2.2	21	81	11	51	55	4	2	38	1.31
44645596--44645635	2	20.0	2	100	0	80	50	0	0	50	1.00
44645713--44645746	17	1.9	17	88	5	50	47	0	2	50	1.16
44648511--44648608	49	2.0	50	89	2	153	43	10	16	29	1.80
44662845--44662870	3	8.7	3	100	0	52	69	0	0	30	0.89
44664059--44664095	18	2.0	19	85	15	51	24	2	8	64	1.34
44664104--44664157	19	2.7	20	83	16	67	35	5	0	59	1.21
44664134--44664209	29	2.6	29	79	8	75	36	2	1	59	1.20
44664071--44664225	9	16.4	9	66	12	62	34	3	1	61	1.20
44664957--44664988	3	10.7	3	100	0	64	31	34	0	34	1.58
44665660--44665693	16	2.1	16	94	0	59	23	52	8	14	1.69
44667393--44667441	17	3.0	16	82	11	64	53	28	0	18	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44668288--44668347	26	2.5	23	79	15	59	30	3	13	53	1.56
44668308--44668354	24	2.0	24	83	8	60	34	4	8	53	1.51
44669464--44669503	20	1.9	22	85	10	57	55	0	0	45	0.99
44673904--44674013	49	2.2	49	80	0	139	27	20	24	28	1.99
44679210--44679465	136	1.9	136	96	0	476	40	12	8	39	1.72
44680020--44680180	86	1.9	86	86	0	232	39	19	18	22	1.93
44680020--44680201	86	2.1	86	84	0	229	39	20	18	22	1.93
44680043--44680266	86	2.6	86	80	0	223	40	20	16	23	1.91
44680020--44680301	43	6.6	43	74	0	186	40	20	17	22	1.92
44689600--44689686	43	2.0	43	82	6	104	29	17	13	39	1.88
44690547--44690579	13	2.5	13	90	9	50	51	0	3	45	1.16
44690570--44690602	17	1.9	18	88	11	52	42	9	0	48	1.35
44693403--44693810	54	7.6	54	82	3	450	38	22	17	22	1.93
44693403--44693811	81	5.1	80	81	6	445	38	22	17	22	1.93
44693403--44693811	27	15.3	26	82	4	392	38	22	17	22	1.93
44693970--44694024	26	2.1	26	89	0	83	21	20	21	36	1.95
44694132--44694192	28	2.2	27	91	2	95	22	22	22	31	1.99
44694157--44694225	33	2.1	34	86	2	95	21	23	26	28	1.99
44705545--44705589	20	2.2	20	100	0	90	71	0	13	15	1.15
44707212--44707273	31	2.0	31	96	0	115	41	9	11	37	1.74
44712372--44712538	25	7.1	22	76	18	160	28	12	14	44	1.81
44712372--44712628	47	5.5	47	88	3	340	28	13	15	43	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44718579--44718658	22	3.5	22	79	17	90	30	10	15	45	1.78
44718633--44718691	31	1.9	31	96	0	109	32	10	11	45	1.74
44718586--44718738	78	2.0	78	96	0	279	29	9	14	46	1.76
44718664--44718799	25	5.8	22	70	20	71	27	12	15	44	1.82
44718664--44718784	47	2.6	47	86	1	154	28	11	15	44	1.81
44718712--44718818	46	2.3	46	82	6	117	28	14	15	40	1.88
44722278--44722308	3	10.3	3	92	0	53	64	35	0	0	0.94
44730641--44730682	2	21.0	2	100	0	84	50	0	0	50	1.00
44731436--44731600	43	3.8	44	73	7	126	30	25	18	25	1.98
44733613--44733664	20	2.5	21	81	15	63	25	5	3	65	1.32
44743131--44743176	14	3.2	14	77	17	58	2	54	0	43	1.12
44750440--44750532	23	4.0	23	84	0	123	39	21	17	21	1.92
44751154--44751191	19	2.0	19	100	0	76	57	10	5	26	1.53
44751467--44751518	27	2.0	25	85	14	70	5	17	5	71	1.26
44751517--44751543	14	1.9	14	100	0	54	22	11	0	66	1.22
44755554--44755607	16	3.2	16	89	5	81	1	51	0	46	1.11
44757359--44757404	6	7.5	6	92	2	74	15	0	13	71	1.14
44757340--44757414	6	13.6	5	86	10	62	14	1	9	74	1.12
44757358--44757414	18	3.2	18	87	7	82	15	0	10	73	1.09
44758699--44758746	24	2.0	24	100	0	96	29	20	16	33	1.95
44760390--44760458	19	3.6	19	76	9	61	57	1	0	40	1.07
44760758--44760798	21	2.0	21	95	0	73	56	12	9	21	1.65
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44763428--44763478	20	2.7	18	80	14	57	31	5	3	58	1.40
44763428--44763478	19	2.7	19	82	14	61	31	5	3	58	1.40
44763511--44763567	10	5.7	10	81	6	53	28	1	3	66	1.18
44763623--44763669	19	2.5	19	77	19	53	31	6	4	57	1.43
44770806--44770998	96	2.0	96	90	2	307	49	4	12	33	1.62
44783746--44783812	33	2.0	33	97	0	125	31	23	10	34	1.89
44793899--44793937	2	20.0	2	89	5	62	53	0	0	46	1.00
44793934--44793992	23	2.4	23	86	8	73	59	3	1	35	1.24
44811716--44811797	31	2.7	31	84	7	105	32	9	10	46	1.72
44812119--44812171	23	2.2	24	83	3	63	62	1	1	33	1.17
44819150--44819196	21	2.2	22	92	3	78	23	17	36	23	1.95
44822049--44822085	16	2.3	16	100	0	74	37	5	35	21	1.77
44822065--44822155	46	2.0	46	93	4	159	26	4	30	38	1.76
44822065--44822172	46	2.5	44	84	11	136	28	3	30	37	1.75
44822314--44822353	17	2.4	17	95	4	73	62	0	0	37	0.95
44822386--44822425	20	2.0	21	85	5	55	60	5	0	35	1.19
44824400--44824458	29	2.0	29	100	0	118	27	10	10	52	1.67
44824821--44824882	25	2.5	25	97	0	115	41	19	9	29	1.83
44825124--44825157	12	2.8	12	100	0	68	61	14	23	0	1.33
44826805--44826830	13	2.0	13	100	0	52	30	15	38	15	1.88
44826955--44827051	45	2.1	46	90	1	151	20	11	50	17	1.76
44843917--44843954	20	1.9	20	88	0	58	18	13	0	68	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
44847121--44847168	13	3.4	14	77	13	53	54	0	0	45	0.99
44847600--44847649	10	5.1	10	79	11	50	52	4	0	44	1.20
44847602--44847649	19	2.5	20	79	3	53	52	4	0	43	1.20
44848779--44848871	40	2.3	40	88	3	134	38	20	19	21	1.93
44848933--44848997	32	2.0	33	84	3	87	30	27	0	41	1.56
44850088--44850133	18	2.4	18	85	10	56	45	0	6	47	1.28
44855008--44855066	12	4.8	12	76	15	50	33	1	1	62	1.15
44855014--44855066	7	7.1	8	80	16	53	33	1	1	62	1.17
44855019--44855066	15	3.2	15	77	16	55	33	2	2	62	1.18
44855159--44855204	2	23.0	2	100	0	92	50	0	0	50	1.00

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