genome.fa.s8.2.7.7.80.10.50.1000.99.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   

This is table  99  of  190  ( 22705 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)
29933248--29933298	21	2.4	21	81	12	61	11	0	49	39	1.40
29933313--29933406	28	3.4	28	88	2	136	25	22	23	28	1.99
29933310--29933429	28	3.9	32	70	27	89	25	22	24	28	1.99
29934772--29934797	5	5.2	5	100	0	52	38	19	19	23	1.93
29935164--29935205	22	1.9	22	90	0	66	61	28	0	9	1.27
29937250--29937334	39	2.2	40	89	4	136	34	12	16	36	1.87
29947239--29947287	20	2.5	20	89	0	71	22	24	0	53	1.47
29947943--29948235	40	7.3	40	86	1	363	41	27	15	15	1.87
29948715--29948779	22	3.0	22	93	0	103	29	16	27	26	1.97
29952076--29952131	25	2.2	25	83	0	67	21	28	19	30	1.98
29952087--29952179	25	3.8	25	77	9	75	19	25	22	32	1.97
29952138--29952241	49	2.1	49	80	3	111	20	26	21	31	1.98
29959980--29960038	26	2.3	26	84	0	82	15	20	27	37	1.92
29960017--29960156	73	1.9	73	80	8	160	22	24	20	33	1.97
29960103--29960169	24	2.8	23	75	6	62	19	25	19	35	1.95
29968250--29968292	17	2.4	18	76	3	52	44	41	4	9	1.57
29970422--29970669	50	4.9	50	79	6	234	23	28	20	27	1.99
29977959--29978206	50	4.9	50	80	6	234	22	28	20	28	1.99
29999208--29999256	24	2.0	24	96	0	89	65	8	6	20	1.41
30006942--30006971	9	3.3	9	90	0	51	36	0	16	46	1.47
30006940--30006994	18	2.9	19	78	10	67	30	0	20	49	1.49
30017211--30017249	20	2.0	20	84	0	51	51	7	15	25	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30019169--30019237	23	2.9	23	85	10	77	66	0	0	33	0.92
30019171--30019239	16	4.3	15	74	17	59	66	0	0	33	0.92
30019169--30019239	24	2.9	24	83	10	83	66	0	0	33	0.92
30025882--30025927	19	2.4	20	85	7	69	45	4	0	50	1.21
30029905--30029955	10	4.6	11	77	15	52	49	13	0	37	1.43
30044065--30044098	17	1.9	18	94	5	61	11	20	44	23	1.84
30044329--30044690	81	4.5	80	82	7	394	43	20	15	20	1.87
30044329--30044697	54	6.8	54	79	7	376	43	20	15	20	1.87
30044329--30044697	27	13.6	27	76	10	335	43	20	15	20	1.87
30044934--30045014	26	3.1	27	80	7	96	20	22	23	33	1.97
30045115--30045218	28	3.5	28	77	17	104	23	23	25	28	1.99
30052530--30053158	210	3.0	210	91	1	1019	36	8	17	37	1.80
30053963--30054585	210	3.0	209	88	4	947	36	8	16	38	1.80
30056247--30056304	19	2.7	22	74	17	59	31	0	10	58	1.31
30062999--30063071	25	2.9	25	83	0	92	28	21	20	28	1.98
30071467--30071510	21	2.1	21	84	12	56	29	6	0	63	1.20
30077164--30077315	3	50.7	3	68	12	64	28	5	3	61	1.37
30087785--30087825	14	3.1	14	79	10	50	75	2	0	21	0.92
30088665--30088743	25	3.2	25	87	7	101	37	2	0	59	1.11
30091865--30091928	27	2.4	27	86	2	94	34	17	9	39	1.82
30093795--30093925	67	2.0	67	89	0	199	28	24	19	27	1.99
30096000--30096156	41	3.8	41	83	2	190	20	31	15	32	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30105179--30105235	30	1.9	30	96	0	105	31	14	22	31	1.93
30111892--30112076	50	3.6	50	80	8	167	28	19	27	24	1.99
30115455--30115490	15	2.5	14	86	8	54	11	8	11	69	1.37
30122897--30122933	16	2.3	16	95	0	65	43	5	27	24	1.76
30122913--30123002	45	2.0	44	87	6	128	31	5	27	35	1.80
30123126--30123158	11	3.0	11	91	8	50	57	0	0	42	0.98
30123103--30123216	20	5.1	21	69	19	79	55	0	0	42	1.12
30123116--30123253	57	2.4	57	83	9	154	53	2	0	44	1.12
30123536--30123687	77	2.0	77	97	0	286	40	8	7	42	1.64
30130076--30130127	2	26.0	2	96	0	95	48	0	0	51	1.00
30130294--30130368	9	8.3	9	70	15	57	25	0	2	72	0.98
30130302--30130369	35	2.0	34	85	2	91	25	0	2	72	0.99
30130534--30130563	4	7.5	4	100	0	60	23	0	26	50	1.50
30131388--30131443	28	2.0	28	100	0	112	32	10	17	39	1.84
30136078--30136116	11	3.5	11	83	16	53	38	2	0	58	1.12
30142882--30142922	16	2.3	19	88	12	61	46	21	0	31	1.52
30142971--30143022	25	2.1	25	100	0	104	26	15	17	40	1.89
30160086--30160115	14	2.1	15	93	6	53	63	0	0	36	0.95
30164590--30165237	322	2.0	322	97	0	1215	28	10	20	41	1.84
30171461--30171527	3	22.3	3	100	0	134	32	0	0	67	0.91
30172206--30172273	22	3.1	22	85	2	93	30	4	45	19	1.70
30176604--30176697	44	2.1	44	92	4	152	35	30	5	28	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30176679--30176714	16	2.2	16	95	0	63	25	33	2	38	1.70
30176957--30177024	21	3.2	21	80	15	77	36	41	0	22	1.54
30176974--30177028	28	2.0	28	85	0	74	38	40	0	21	1.54
30177389--30177747	41	8.9	41	80	4	381	32	29	17	21	1.96
30177389--30177742	81	4.4	79	78	10	335	32	28	17	21	1.96
30177389--30177742	122	2.9	122	84	3	457	32	28	17	21	1.96
30188852--30188887	15	2.5	14	86	8	54	44	8	2	44	1.48
30190699--30190825	61	2.1	61	80	0	137	40	15	7	36	1.75
30191783--30192131	123	2.8	124	92	1	585	29	15	22	32	1.94
30195322--30195492	29	6.4	27	73	18	112	29	0	23	46	1.53
30195322--30195403	29	2.8	29	96	0	146	28	0	26	45	1.54
30195313--30195540	101	2.3	100	94	2	402	32	0	21	45	1.52
30195425--30195506	29	2.8	29	92	0	137	28	0	23	48	1.51
30195353--30195486	72	1.9	72	88	3	207	31	0	22	46	1.52
30196685--30196709	7	3.6	7	100	0	50	60	12	0	28	1.32
30197786--30197851	31	2.1	32	94	2	116	68	0	0	31	0.90
30197854--30197965	51	2.2	51	91	0	179	42	1	26	28	1.65
30197940--30197987	22	2.2	22	100	0	96	41	0	33	25	1.55
30229706--30230063	177	2.0	177	93	0	617	27	12	23	36	1.91
30236356--30236385	16	1.9	16	93	6	53	50	20	0	30	1.49
30236852--30236881	16	1.9	16	93	6	53	20	23	0	56	1.42
30236834--30236875	20	2.2	19	83	12	50	16	19	0	64	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30248283--30248490	115	1.8	115	91	0	344	40	18	20	20	1.92
30248416--30248562	72	2.0	72	90	2	233	40	17	17	23	1.90
30249713--30249891	45	4.0	45	83	4	202	21	13	26	37	1.91
30249707--30249885	90	2.0	88	83	2	223	21	13	27	36	1.92
30253378--30253409	15	2.1	15	94	0	55	15	6	9	68	1.36
30257446--30257482	13	2.8	13	100	0	74	24	32	13	29	1.93
30264611--30264648	20	1.9	20	88	0	58	13	23	23	39	1.90
30277222--30277263	16	2.6	16	84	0	57	57	0	4	38	1.20
30278995--30279032	6	6.3	6	82	11	51	18	2	0	78	0.86
30279041--30279637	299	2.0	299	97	0	1122	29	11	19	39	1.87
30280067--30280093	2	13.5	2	100	0	54	51	0	48	0	1.00
30280309--30280348	21	1.9	21	85	10	55	47	20	7	25	1.75
30283447--30283491	22	2.0	22	83	12	56	31	15	4	48	1.65
30284441--30284577	68	2.0	68	94	0	238	35	22	16	25	1.94
30296511--30296628	61	2.0	61	86	5	168	38	21	6	33	1.80
30301447--30301478	15	2.1	15	100	0	64	31	6	0	62	1.20
30302193--30302239	18	2.6	18	89	3	67	19	23	27	29	1.98
30302206--30302245	18	2.2	18	86	0	53	22	27	27	22	1.99
30302156--30302261	55	1.9	56	86	1	151	21	21	25	31	1.98
30304282--30304320	16	2.3	19	79	20	50	43	5	5	46	1.48
30304569--30304744	75	2.3	77	87	4	259	48	9	9	33	1.66
30304569--30305177	77	8.0	77	73	15	321	43	9	10	37	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30304977--30305107	67	2.0	67	86	3	183	40	6	13	38	1.72
30305566--30305664	17	5.9	17	73	11	80	31	0	2	66	1.03
30305550--30305710	49	3.2	49	88	3	214	31	1	3	63	1.17
30310921--30311069	75	2.0	77	80	5	169	46	8	11	33	1.69
30311270--30311302	16	2.1	16	94	0	57	54	0	0	45	0.99
30313521--30313743	69	3.3	69	86	3	283	40	6	19	33	1.77
30315335--30315390	17	3.3	17	76	0	58	19	3	3	73	1.13
30315347--30315390	13	3.4	13	81	6	54	20	4	0	75	0.98
30315728--30315778	19	3.1	16	81	13	59	15	3	3	76	1.08
30315747--30315786	19	2.0	20	86	13	57	15	2	10	72	1.21

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