genome.fa.s4.2.7.7.80.10.50.1000.125.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  125  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)
40048714--40049165	150	3.0	149	85	1	584	33	21	18	26	1.96
40054632--40054668	14	2.5	14	91	8	56	59	0	40	0	0.97
40054629--40054678	20	2.8	17	77	16	55	64	0	36	0	0.94
40054864--40055003	41	3.2	43	75	16	121	29	0	14	55	1.44
40054901--40055265	49	7.6	49	77	13	334	32	0	14	52	1.47
40054933--40055219	27	11.7	27	75	18	265	31	1	13	54	1.46
40054933--40055219	76	3.9	74	83	11	335	31	1	13	54	1.46
40055149--40055198	22	2.5	19	76	17	55	32	2	14	52	1.53
40055415--40055495	38	2.2	38	95	2	146	54	3	2	39	1.32
40055532--40055573	16	2.7	15	85	7	57	35	2	4	57	1.33
40057684--40057728	22	2.1	21	91	4	72	0	33	2	64	1.06
40057789--40057864	27	2.8	27	86	7	109	19	36	26	17	1.94
40065398--40065697	45	6.7	44	77	9	198	44	16	19	20	1.87
40065480--40065548	21	3.1	22	67	19	61	43	14	18	23	1.87
40065397--40065694	90	3.3	90	77	9	277	43	15	19	20	1.87
40072434--40072482	19	2.4	19	83	10	62	36	4	2	57	1.30
40072436--40072474	19	2.0	21	90	10	64	38	5	2	53	1.37
40078186--40078239	28	2.0	27	82	13	67	57	27	0	14	1.38
40081843--40081917	37	2.1	37	92	2	125	42	28	12	17	1.84
40083005--40083101	48	2.0	48	95	0	176	34	19	9	37	1.84
40088767--40088850	22	3.8	22	93	0	132	32	13	26	28	1.93
40089058--40089097	21	1.9	21	84	0	53	50	15	2	32	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40093679--40093728	22	2.4	22	86	6	68	62	8	4	26	1.41
40101814--40101859	20	2.3	20	85	7	58	45	23	4	26	1.71
40104030--40104257	112	2.0	112	93	0	393	32	13	25	28	1.94
40107358--40107442	43	2.0	42	93	2	143	17	5	27	49	1.69
40113273--40113328	11	4.8	11	79	12	58	58	12	0	28	1.34
40114974--40115010	18	2.1	18	85	14	51	37	0	8	54	1.30
40116346--40116392	24	1.9	24	83	12	60	31	6	6	55	1.51
40116418--40116469	10	5.0	10	75	9	50	19	7	1	71	1.20
40116419--40116463	20	2.2	20	84	7	56	17	8	2	71	1.23
40116461--40116497	2	18.5	2	94	0	65	45	0	0	54	1.00
40122046--40122106	32	1.9	32	96	0	113	21	22	36	19	1.95
40127778--40128158	42	9.1	42	85	1	478	22	18	22	36	1.95
40127778--40128158	126	3.0	125	88	1	539	22	18	22	36	1.95
40128924--40129395	148	3.2	147	80	8	419	43	4	10	41	1.60
40130945--40130988	21	2.1	21	83	8	54	29	0	15	54	1.42
40133414--40133466	16	3.5	16	75	15	67	58	20	1	18	1.49
40133412--40133467	29	1.9	29	100	0	112	60	19	1	17	1.45
40144695--40144754	26	2.3	26	88	0	84	36	1	1	60	1.17
40147816--40147848	17	1.9	17	93	0	57	60	0	9	30	1.27
40149404--40149453	22	2.2	24	79	13	61	40	4	2	54	1.31
40150116--40150150	16	2.2	16	89	0	52	51	5	17	25	1.67
40150354--40150437	16	4.9	16	69	20	55	42	1	0	55	1.07
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40167084--40167114	3	10.7	3	93	6	55	70	0	0	29	0.87
40167730--40168331	44	13.8	45	71	15	279	28	23	19	28	1.99
40167834--40168417	217	2.7	217	94	1	999	28	23	19	28	1.98
40167736--40168237	261	1.9	261	80	8	576	28	23	20	27	1.99
40173559--40173610	27	2.0	26	84	3	68	5	32	9	51	1.58
40180381--40180435	17	3.3	17	71	19	53	69	9	5	16	1.34
40182169--40182211	16	2.6	17	83	16	56	39	4	2	53	1.34
40190227--40190292	28	2.4	28	78	0	78	34	18	0	46	1.49
40190247--40190294	7	6.9	7	80	0	60	31	14	0	54	1.41
40190316--40190345	15	1.9	16	93	6	53	20	13	0	66	1.24
40196240--40196279	20	2.0	20	95	0	71	32	25	12	30	1.92
40201900--40201931	16	2.0	16	100	0	64	25	18	25	31	1.98
40204340--40204492	46	3.2	46	65	10	128	30	20	26	23	1.99
40204335--40204600	96	2.7	96	90	3	390	28	21	24	24	1.99
40211744--40211774	13	2.5	13	94	5	55	38	9	16	35	1.81
40212178--40212220	21	2.0	21	100	0	86	32	9	13	44	1.76
40212453--40212493	6	6.8	6	94	0	55	17	65	12	4	1.42
40213818--40213855	6	6.5	6	96	3	69	68	0	0	31	0.90
40213840--40213900	21	3.0	21	76	7	54	45	0	0	54	1.00
40213864--40213940	10	7.8	10	73	2	66	36	0	0	63	0.95
40213861--40213943	30	2.8	30	96	1	150	38	0	0	61	0.96
40218412--40218437	2	13.0	2	100	0	52	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40219303--40219376	31	2.5	29	80	8	78	35	1	0	63	1.03
40220814--40220843	10	2.9	10	95	5	51	60	0	0	40	0.97
40221335--40221471	43	3.2	42	86	4	184	29	23	21	25	1.99
40221335--40221564	42	5.2	42	80	13	191	28	22	23	26	1.99
40221490--40221582	42	2.2	43	92	1	152	27	23	20	27	1.99
40222004--40222072	21	3.3	21	83	0	75	2	39	20	37	1.68
40227542--40227792	9	29.8	9	73	12	167	30	2	19	47	1.64
40227531--40227734	25	8.1	25	82	2	237	30	2	20	46	1.65
40227603--40227772	41	4.3	41	77	15	187	30	2	18	48	1.63
40227603--40227750	16	9.0	16	75	14	124	30	2	19	47	1.63
40227690--40227806	25	5.0	24	71	23	79	29	1	17	52	1.54
40227779--40227874	48	2.0	48	100	0	192	31	2	16	50	1.57
40227794--40227880	24	3.6	24	71	17	81	32	2	14	50	1.56
40227931--40227985	24	2.2	26	83	6	69	21	1	18	58	1.49
40228159--40228191	15	2.2	15	94	0	57	54	3	3	39	1.31
40229392--40229448	24	2.5	22	81	13	69	38	3	42	15	1.65
40229985--40230037	22	2.5	22	93	3	90	37	28	3	30	1.75
40229998--40230083	29	2.9	29	76	8	93	38	31	2	27	1.70
40230005--40230053	15	3.4	14	77	5	53	40	26	2	30	1.67
40230841--40230987	77	1.9	76	83	4	188	29	17	19	32	1.95
40230631--40231425	266	3.0	266	93	2	1397	29	19	19	32	1.96
40231405--40231645	113	2.1	113	80	5	261	29	21	21	27	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40231480--40231781	113	2.7	113	81	4	324	29	19	23	27	1.98
40232076--40232103	8	3.5	8	100	0	56	32	10	0	57	1.33
40238523--40238663	11	13.5	11	73	18	106	59	0	2	37	1.14
40238566--40238599	17	2.0	17	88	0	50	64	0	0	35	0.94
40238523--40238680	40	3.8	40	88	9	214	61	0	1	36	1.12
40238536--40238663	52	2.5	51	86	8	163	60	0	2	36	1.09
40238825--40238873	22	2.2	22	100	0	98	4	51	40	4	1.40
40239501--40239545	3	15.0	3	100	0	90	33	0	0	66	0.92
40240154--40240198	25	2.0	24	83	16	60	55	11	2	31	1.47
40241260--40241511	36	7.1	36	62	4	116	33	19	23	23	1.97
40241263--40241558	71	4.2	71	78	0	304	32	19	23	24	1.98
40250331--40250417	41	2.1	41	85	6	115	62	11	0	26	1.29
40259488--40259533	23	2.0	23	86	0	65	26	32	4	36	1.76
40263040--40263171	67	2.0	67	90	0	210	27	28	18	25	1.98
40272828--40272931	31	3.4	31	93	0	181	17	40	25	16	1.90
40272880--40272931	18	3.2	18	66	25	51	15	42	26	15	1.87
40287196--40287253	17	3.3	18	77	17	52	41	0	0	58	0.98
40288910--40288969	24	2.5	25	75	8	61	50	6	0	43	1.28
40292570--40292669	25	4.0	25	74	5	69	21	24	18	37	1.94
40293444--40293840	133	3.0	133	97	0	749	30	5	25	38	1.77
40294539--40294582	17	2.6	17	82	10	63	45	0	11	43	1.40
40294571--40294603	9	3.7	9	95	0	57	36	0	6	57	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40300307--40300370	20	3.1	19	79	16	65	71	3	1	23	1.08
40300326--40300376	23	2.1	25	82	13	63	70	3	0	25	1.04
40302762--40302880	51	2.3	51	82	2	132	31	21	7	39	1.81
40303810--40303844	15	2.4	15	90	4	54	48	0	8	42	1.33
40308429--40308463	18	1.9	18	88	11	54	62	5	0	31	1.18
40310243--40310288	12	3.9	12	75	13	51	21	6	0	71	1.08
40311310--40311370	16	3.8	16	76	20	56	75	1	1	21	0.98
40311310--40311356	10	4.7	10	79	7	51	74	2	0	23	0.93
40313483--40313573	40	2.3	40	90	0	137	42	7	20	28	1.80
40313503--40313586	40	2.1	40	81	0	96	44	11	16	27	1.83

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