genome.fa.s4.2.7.7.80.10.50.1000.19.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  19  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)
5696960--5697015	22	2.5	22	97	2	103	41	0	26	32	1.56
5699336--5699420	19	4.6	18	73	21	59	63	3	3	29	1.28
5699346--5699399	21	2.7	19	78	10	63	64	1	0	33	1.04
5699346--5699400	10	5.5	10	71	16	51	63	1	0	34	1.05
5699887--5699916	2	15.0	2	100	0	60	50	0	0	50	1.00
5700150--5700188	20	2.0	20	100	0	78	38	0	0	61	0.96
5705365--5705428	22	2.8	22	81	11	67	57	0	0	42	0.98
5707478--5707502	11	2.3	11	100	0	50	24	0	28	48	1.52
5718951--5718990	18	2.2	18	86	8	55	67	7	0	25	1.16
5720376--5720413	17	2.2	18	86	13	53	26	2	2	68	1.16
5720596--5720670	17	4.5	17	70	25	54	58	0	5	36	1.21
5728051--5728273	9	25.0	9	72	7	134	44	14	4	35	1.66
5728039--5728211	27	6.1	27	81	14	195	46	12	2	38	1.54
5728075--5728163	36	2.5	36	94	3	153	47	10	3	39	1.54
5745488--5745739	126	2.0	124	88	1	369	24	19	22	32	1.97
5745488--5745738	42	6.0	42	84	5	312	24	19	22	33	1.97
5745828--5745870	22	2.0	22	90	0	68	48	27	13	9	1.73
5747111--5747136	8	3.2	8	100	0	52	34	0	0	65	0.93
5747830--5747920	17	5.4	17	72	21	75	37	2	0	60	1.09
5747837--5747891	13	4.2	13	72	21	51	38	3	0	58	1.16
5747817--5747924	38	2.8	36	80	13	101	37	2	0	59	1.12
5747829--5747885	29	2.0	28	93	6	98	38	1	0	59	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5747849--5747921	10	7.8	10	72	15	59	38	1	0	60	1.06
5747891--5747965	33	2.3	32	84	11	98	37	0	1	61	1.05
5748432--5748510	29	2.7	30	80	11	92	43	10	13	32	1.78
5757772--5758212	51	8.7	51	75	6	346	28	16	25	29	1.96
5757772--5758216	102	4.4	102	88	5	575	28	16	25	29	1.96
5760208--5760263	17	3.2	16	82	14	58	62	0	0	37	0.95
5762079--5762345	89	3.0	89	83	4	304	36	17	10	34	1.85
5762844--5762928	29	2.8	30	75	10	77	63	1	4	30	1.22
5762779--5762934	9	16.3	9	66	23	54	62	1	6	29	1.31
5762888--5762934	19	2.4	19	82	3	58	70	0	4	25	1.05
5763363--5763556	90	2.1	94	82	5	234	41	8	17	32	1.79
5765556--5766421	251	3.5	248	88	3	1247	31	16	17	34	1.92
5770817--5770891	21	3.6	21	87	0	87	21	10	38	29	1.87
5770964--5771111	30	5.0	30	78	4	149	34	23	4	37	1.74
5771446--5771539	7	13.3	7	80	8	75	74	0	25	0	0.82
5771444--5771539	14	6.8	14	79	13	83	73	0	26	0	0.83
5771444--5771518	8	8.0	9	77	16	57	73	0	26	0	0.84
5771820--5771849	8	3.6	8	91	8	51	80	0	20	0	0.72
5771815--5771859	18	2.6	18	89	3	65	82	0	17	0	0.68
5771819--5771863	17	2.5	18	85	10	65	80	0	20	0	0.72
5772200--5772240	22	1.9	21	90	5	64	39	12	9	39	1.76
5772181--5772257	39	2.1	36	85	7	100	37	7	12	41	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5772178--5772484	17	17.4	18	75	14	248	30	11	12	45	1.77
5772178--5772510	35	9.4	34	75	9	244	30	12	12	45	1.77
5772178--5772545	17	21.1	17	72	13	239	31	11	11	45	1.77
5776013--5776078	7	9.1	7	93	3	105	45	39	0	15	1.46
5779956--5780042	1	87.0	1	72	0	57	85	5	8	1	0.80
5779956--5780042	15	5.5	15	78	8	84	85	5	8	1	0.80
5779956--5780042	16	5.5	16	75	2	70	85	5	8	1	0.80
5779956--5780042	18	4.8	19	77	7	74	85	5	8	1	0.80
5779964--5780041	8	9.9	8	77	12	63	84	5	8	1	0.82
5780893--5781670	230	3.4	228	80	9	799	27	16	21	35	1.94
5780911--5781747	153	5.4	151	83	7	863	27	16	21	34	1.94
5780903--5781747	77	10.9	76	81	9	883	27	16	21	35	1.94
5781927--5782075	30	5.0	29	83	3	163	34	22	4	38	1.73
5781934--5782050	59	2.0	60	87	1	173	35	23	2	38	1.69
5782409--5782497	7	13.3	7	80	16	66	76	0	22	1	0.85
5782407--5782496	14	6.5	14	79	12	80	75	0	23	1	0.87
5782442--5782505	7	8.4	7	81	14	74	82	0	17	0	0.66
5782442--5782506	12	5.2	13	77	15	66	83	0	16	0	0.66
5782442--5782506	8	8.4	8	81	10	73	83	0	16	0	0.66
5782407--5782506	27	3.7	27	78	17	102	77	0	22	1	0.84
5782788--5782817	8	3.6	8	91	8	51	80	0	20	0	0.72
5782784--5782827	18	2.6	18	85	7	65	84	0	15	0	0.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5782787--5782831	17	2.5	18	85	10	65	80	0	20	0	0.72
5783183--5783224	21	2.0	21	85	0	57	45	9	7	38	1.64
5783168--5783241	38	1.9	38	88	0	112	35	9	10	44	1.72
5783146--5783509	17	20.9	17	73	11	247	32	11	11	45	1.75
5783150--5783494	35	9.9	34	75	11	256	31	11	11	45	1.75
5783442--5783502	32	1.9	32	93	0	104	40	6	8	44	1.60
5791997--5792036	15	2.8	14	85	7	62	35	5	5	55	1.44
5792357--5792421	26	2.6	23	73	21	60	67	0	0	32	0.91
5792368--5792416	19	2.8	16	82	14	53	61	0	0	38	0.96
5792433--5792462	2	15.0	2	100	0	60	50	0	0	50	1.00
5794469--5794617	38	3.9	38	73	8	104	60	1	4	34	1.24
5794450--5794613	10	17.2	9	70	17	75	59	1	4	34	1.26
5794567--5794617	19	2.6	20	81	12	61	64	0	3	31	1.11
5795039--5795218	95	1.9	93	85	2	243	34	8	19	37	1.83
5795070--5795266	87	2.2	92	81	9	217	38	8	18	35	1.80
5797327--5797937	248	2.5	248	94	0	1062	32	16	17	33	1.92
5803416--5803462	9	5.2	9	80	10	60	40	0	0	59	0.97
5803404--5803469	27	2.4	27	89	2	105	42	0	0	57	0.98
5805194--5805251	19	3.2	19	85	7	75	62	0	1	36	1.06
5805207--5805257	19	2.7	18	88	8	75	60	0	1	37	1.08
5806284--5806323	16	2.5	16	95	0	71	42	17	15	25	1.88
5807334--5807419	10	8.8	10	74	11	63	62	2	3	31	1.24
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5807356--5807409	19	2.8	19	84	13	67	62	1	1	33	1.16
5807333--5807427	29	3.2	30	76	11	108	63	2	3	31	1.22
5807329--5807427	19	5.1	19	69	21	64	64	2	3	30	1.20
5810139--5810747	248	2.4	247	89	4	908	33	15	17	33	1.92
5816232--5816257	4	6.5	4	100	0	52	73	0	0	26	0.84
5816724--5816758	18	1.9	18	88	0	52	28	2	11	57	1.48
5817419--5817573	19	8.2	19	70	18	67	59	1	7	31	1.35
5817474--5817520	10	4.8	10	76	12	53	59	2	2	36	1.21
5818037--5818220	84	2.2	85	82	9	223	36	7	16	39	1.76
5822457--5822494	20	1.9	20	84	10	51	57	0	5	36	1.21
5823067--5823116	14	3.6	14	78	7	50	38	42	4	16	1.66
5823054--5823118	28	2.3	27	80	12	69	36	41	4	16	1.70
5831198--5831351	77	2.0	77	91	2	247	30	15	29	24	1.96
5832748--5832777	15	2.0	15	100	0	60	46	20	13	20	1.83
5837816--5837885	34	2.1	34	91	0	113	31	15	20	32	1.94
5840422--5840496	35	2.1	36	82	7	91	48	1	0	50	1.09
5840489--5840518	14	2.1	15	93	6	53	56	0	0	43	0.99
5843247--5843311	22	2.9	22	80	14	71	56	4	4	33	1.40
5845363--5845698	46	7.6	46	88	8	475	28	22	14	33	1.94
5845544--5845616	36	2.0	36	94	0	128	26	20	15	38	1.92
5845498--5845662	82	2.0	82	93	0	285	27	21	14	35	1.93
5845452--5845698	128	1.9	128	94	0	431	28	22	13	34	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5848322--5848905	132	4.4	132	89	1	857	26	25	19	29	1.98
5848322--5848913	263	2.2	264	88	0	873	27	25	18	29	1.98
5849027--5849351	45	7.3	44	71	10	223	28	26	16	27	1.97
5849021--5849363	88	3.9	88	80	4	334	28	26	17	27	1.98
5850609--5850726	62	1.9	62	87	3	175	11	24	13	50	1.75
5867367--5867468	43	2.4	44	84	9	124	22	18	28	30	1.97
5867629--5867660	16	1.9	17	93	6	57	40	0	21	37	1.54
5875839--5875884	23	2.0	23	84	12	60	34	15	19	30	1.93
5892660--5892789	43	3.0	43	77	16	142	23	18	29	28	1.98
5895401--5895444	23	1.9	23	85	0	61	29	2	6	61	1.34

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