genome.fa.s4.2.7.7.80.10.50.1000.34.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  34  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)
9927864--9927965	28	3.5	28	69	17	80	16	19	38	25	1.92
9927831--9927950	61	2.0	61	91	0	195	16	19	36	27	1.93
9950531--9950582	18	2.9	18	77	11	61	25	34	7	32	1.84
9984239--9984279	19	2.2	19	86	0	55	34	17	26	21	1.95
9984606--9984701	17	5.6	17	71	22	67	38	2	4	55	1.31
9984740--9984786	23	2.0	24	84	12	62	44	0	8	46	1.33
9986984--9987146	87	1.9	86	86	6	231	28	15	19	35	1.93
9989560--9989592	7	4.7	7	100	0	66	87	0	0	12	0.53
9995967--9996040	36	2.1	36	86	0	103	29	13	17	39	1.88
10002408--10002432	12	2.1	12	100	0	50	84	0	0	16	0.63
10012444--10012482	18	2.2	18	100	0	78	20	5	28	46	1.72
10016432--10016479	24	2.0	24	84	4	62	27	18	2	52	1.57
10017613--10017655	22	2.0	22	100	0	86	37	13	25	23	1.92
10034024--10034066	19	2.3	19	83	0	59	32	27	13	25	1.94
10045313--10045365	23	2.2	24	93	3	90	47	0	7	45	1.31
10057213--10057294	22	3.7	22	86	0	119	29	25	14	30	1.95
10066867--10066915	24	2.0	24	88	0	71	8	26	40	24	1.83
10067823--10067847	13	1.9	13	100	0	50	8	0	24	68	1.16
10069478--10069593	41	2.8	42	92	2	182	27	19	29	23	1.98
10069477--10069613	41	3.3	41	81	6	170	30	18	27	23	1.98
10071664--10071976	155	2.0	154	88	3	459	42	14	10	33	1.79
10073231--10073701	158	3.0	158	88	0	703	38	10	9	41	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10074562--10074591	12	2.5	12	100	0	60	23	10	23	43	1.83
10075366--10075415	13	3.8	13	79	7	57	20	8	14	58	1.61
10087738--10087777	17	2.3	18	86	4	55	45	2	2	50	1.28
10087662--10087968	155	2.0	157	88	3	469	40	12	7	40	1.71
10088968--10089001	12	2.8	12	86	0	50	29	20	35	14	1.93
10092440--10092482	18	2.4	17	85	14	52	46	0	2	51	1.13
10092450--10092486	18	2.1	17	90	10	56	45	0	0	54	1.00
10092564--10092613	23	2.2	23	85	7	66	44	2	8	46	1.44
10092737--10092776	17	2.3	18	86	4	55	45	2	2	50	1.28
10092651--10093128	157	3.0	158	88	3	705	37	10	9	42	1.72
10092889--10092937	16	2.9	16	85	11	55	46	4	8	40	1.52
10093042--10093079	17	2.2	18	85	4	51	44	0	5	50	1.24
10095987--10096425	27	16.4	26	82	5	443	19	16	21	43	1.88
10095987--10096425	54	8.2	52	83	5	495	19	16	21	43	1.88
10095987--10096425	81	5.5	80	86	4	528	19	16	21	43	1.88
10095973--10096401	214	2.0	215	88	5	636	19	16	21	42	1.89
10099127--10099183	27	2.2	26	80	3	60	54	12	8	24	1.65
10114761--10115320	267	2.1	266	89	0	832	29	20	23	26	1.99
10115325--10115447	44	2.8	44	80	6	151	30	20	21	27	1.98
10115390--10115559	78	2.2	78	96	0	322	27	20	23	28	1.99
10115417--10115543	40	3.2	40	68	16	129	26	22	19	31	1.98
10115533--10115649	45	2.7	44	79	12	125	24	19	28	27	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10116462--10116502	17	2.5	16	84	7	55	4	4	12	78	1.07
10125912--10125950	18	2.1	19	85	4	53	35	0	5	58	1.20
10126789--10126840	20	2.7	18	82	14	59	17	0	32	50	1.47
10138622--10138652	6	5.2	6	92	0	53	16	16	3	64	1.42
10139065--10139095	14	2.2	14	94	0	53	61	12	3	22	1.46
10139633--10139707	27	2.8	27	87	0	114	33	36	16	14	1.89
10141349--10141433	42	2.0	42	81	0	98	29	24	30	15	1.95
10141312--10141536	105	2.2	104	80	7	260	24	23	29	22	1.99
10144871--10144910	20	2.0	21	90	5	64	30	5	2	62	1.29
10156941--10157040	45	2.2	43	81	10	119	23	26	12	39	1.89
10159572--10159729	43	3.6	44	83	3	185	23	20	20	34	1.96
10163621--10163664	22	2.0	22	100	0	88	36	4	13	45	1.64
10163647--10163707	30	2.0	30	100	0	122	26	9	9	54	1.64
10163874--10163927	26	2.1	25	86	10	74	9	12	0	77	0.98
10163874--10163926	24	2.1	26	89	6	83	9	13	0	77	0.99
10164833--10164871	21	1.9	20	84	5	51	38	0	2	58	1.12
10167924--10167991	29	2.3	28	82	12	75	10	13	0	76	1.02
10168781--10168825	6	7.7	6	87	7	58	73	0	0	26	0.84
10168774--10168825	11	4.5	11	82	15	61	73	0	1	25	0.94
10168780--10168825	25	1.9	24	91	8	76	73	0	0	26	0.83
10168780--10168819	13	3.2	13	89	3	64	75	0	0	25	0.81
10168774--10168824	18	2.8	18	85	8	68	74	0	1	23	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10180366--10180431	30	2.2	31	86	2	89	50	4	3	42	1.38
10184703--10184956	69	3.7	68	85	4	305	18	23	24	34	1.96
10184897--10185015	59	2.0	59	85	0	157	17	22	21	37	1.94
10184987--10185168	69	2.6	69	80	0	211	20	19	21	37	1.94
10197716--10197754	18	2.2	17	86	4	51	48	12	15	23	1.79
10203754--10203794	20	2.0	22	90	9	68	68	0	0	31	0.90
10206786--10206814	2	14.5	2	100	0	58	0	51	0	48	1.00
10219062--10219087	2	13.0	2	100	0	52	50	0	0	50	1.00
10226619--10226689	33	2.2	33	86	0	97	38	12	8	40	1.74
10226647--10226756	44	2.5	44	92	0	175	33	10	14	40	1.81
10232775--10232813	14	2.8	14	80	0	51	35	10	12	41	1.77
10233002--10233034	16	2.1	16	88	11	50	39	0	3	57	1.14
10233005--10233046	22	2.0	21	86	13	59	38	0	7	54	1.28
10233062--10233111	20	2.4	21	93	6	84	48	0	0	52	1.00
10233062--10233112	10	4.9	10	80	4	57	47	0	0	52	1.00
10233282--10233374	44	2.1	44	88	6	134	37	29	3	30	1.73
10233356--10233394	16	2.4	16	95	0	69	28	30	7	33	1.85
10237194--10237226	7	4.7	7	85	14	50	42	0	0	57	0.98
10243459--10243559	40	2.5	40	87	3	150	33	24	17	23	1.96
10246473--10246539	33	2.0	33	100	0	134	20	16	20	41	1.90
10249728--10249770	21	2.0	21	100	0	86	41	13	4	39	1.66
10249754--10249787	16	2.1	16	88	0	50	35	20	0	44	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10249910--10249993	28	2.9	29	84	7	100	51	9	16	22	1.73
10250382--10250452	33	2.2	32	84	5	88	40	2	15	40	1.62
10256965--10256997	7	4.7	7	96	0	57	45	0	9	45	1.35
10257455--10257498	22	2.1	20	83	8	52	11	6	2	79	1.01
10263260--10263303	23	1.9	22	82	17	54	36	25	0	38	1.56
10263348--10263434	45	1.9	45	90	0	138	34	24	18	22	1.96
10276626--10276663	13	3.0	13	85	14	53	5	15	0	78	0.91
10282133--10282323	43	4.4	43	85	0	247	34	26	14	25	1.94
10282441--10282525	31	2.7	30	78	7	89	41	18	10	29	1.84
10282441--10282536	30	3.1	31	71	13	79	43	18	9	28	1.81
10283984--10284047	31	2.1	31	96	0	119	39	25	6	29	1.80
10288027--10288230	107	1.9	107	92	0	345	50	8	7	34	1.61
10290610--10290634	12	2.1	12	100	0	50	36	0	32	32	1.58
10298723--10298764	20	2.2	19	87	12	59	16	21	4	57	1.58
10304334--10304366	15	2.2	15	94	0	57	36	6	21	36	1.78
10304448--10304509	18	3.2	18	73	15	52	62	6	3	27	1.35
10306053--10306127	17	4.5	16	70	12	62	66	0	0	33	0.92
10315650--10315756	53	2.0	53	94	0	187	24	15	9	50	1.74
10317676--10317726	20	2.6	19	84	9	66	45	15	11	27	1.81
10319936--10319974	20	2.0	20	100	0	78	56	2	0	41	1.13
10325928--10326003	20	3.9	19	81	5	82	44	13	9	32	1.75
10325925--10326002	40	2.0	40	87	7	115	46	12	8	32	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10326858--10326892	17	2.0	18	88	5	54	8	14	11	65	1.46
10333874--10333923	23	2.2	23	92	0	82	44	26	2	28	1.65
10345542--10345580	12	3.2	13	89	10	64	23	0	12	64	1.28
10346768--10346868	43	2.3	44	81	5	125	33	15	26	23	1.95
10350208--10350311	52	2.0	52	90	3	165	27	20	16	35	1.94
10351813--10351952	22	6.3	22	75	5	84	43	22	10	23	1.84
10351785--10351931	69	2.1	69	87	0	204	46	19	10	23	1.81
10351991--10352028	11	3.5	11	85	0	58	50	26	5	18	1.68
10351978--10352028	22	2.3	22	93	0	84	47	25	7	19	1.76
10359568--10359870	22	13.4	22	73	10	216	44	21	11	23	1.84

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