genome.fa.s8.2.7.7.80.10.50.1000.169.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  169  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)
49291723--49291763	22	1.9	22	90	5	66	24	12	4	58	1.53
49291800--49291831	15	2.1	16	88	11	50	31	0	0	68	0.90
49292572--49292596	2	12.5	2	100	0	50	52	0	0	48	1.00
49309734--49309764	4	8.0	4	92	7	55	74	0	0	25	0.82
49310068--49310163	31	3.1	31	95	3	174	45	13	9	31	1.75
49320052--49320113	7	8.3	7	73	19	54	22	0	0	77	0.77
49320052--49320087	13	2.6	14	91	8	56	19	0	0	80	0.71
49320068--49320136	26	2.7	25	82	6	84	30	1	1	66	1.09
49323026--49323417	216	1.8	215	88	3	601	40	10	11	37	1.76
49328742--49328776	16	2.2	16	94	0	61	40	0	8	51	1.33
49331100--49331164	5	13.2	5	78	15	64	41	0	1	56	1.08
49332308--49332372	21	3.1	21	79	0	85	16	23	23	36	1.94
49339686--49339735	5	10.0	5	78	8	57	54	2	0	44	1.11
49339686--49339737	16	3.4	16	82	12	65	53	1	0	44	1.11
49342210--49342238	11	2.5	12	94	5	51	20	0	0	79	0.74
49342299--49342344	3	15.3	3	100	0	92	34	0	0	65	0.93
49345658--49345711	26	2.1	26	100	0	108	37	0	3	59	1.15
49347092--49347121	12	2.5	12	88	0	51	40	0	10	50	1.36
49347419--49347472	26	2.1	26	85	0	72	46	9	12	31	1.74
49350633--49350664	16	2.1	16	94	5	57	59	0	0	40	0.97
49350625--49350677	24	2.1	26	86	10	74	56	0	0	43	0.99
49350635--49350692	24	2.4	22	78	16	53	55	0	3	41	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49350825--49350876	3	17.7	3	96	4	97	34	0	0	65	0.93
49350909--49350950	19	2.2	19	87	12	59	66	7	19	7	1.39
49351404--49351460	3	19.0	3	100	0	114	33	0	0	66	0.92
49352082--49352192	23	5.1	21	78	6	114	20	20	20	37	1.94
49352622--49352760	46	3.0	46	87	4	208	29	26	7	35	1.85
49356345--49356426	42	2.0	42	80	4	94	32	23	12	31	1.91
49356387--49356563	49	3.6	49	88	3	241	31	29	14	24	1.95
49361862--49361909	22	2.2	22	92	0	78	31	6	18	43	1.75
49363424--49363620	54	3.6	53	78	5	189	45	16	12	25	1.82
49363424--49363632	27	7.7	27	71	13	108	44	18	11	25	1.84
49366802--49366884	25	3.5	24	79	6	80	26	10	44	18	1.82
49366810--49366883	25	3.0	25	86	7	105	27	10	43	18	1.83
49367896--49368144	42	5.9	41	89	2	345	30	25	15	28	1.96
49369268--49369301	12	2.8	12	95	0	59	55	5	0	38	1.24
49374122--49374148	12	2.2	12	100	0	54	22	77	0	0	0.76
49376282--49376332	22	2.3	22	80	10	59	33	0	1	64	1.05
49377877--49378175	50	5.8	50	90	2	427	21	30	22	25	1.99
49378270--49378300	13	2.4	13	94	0	53	54	12	0	32	1.38
49378513--49378570	30	1.9	30	89	0	89	31	24	3	41	1.71
49380213--49380265	17	3.2	17	81	5	63	60	3	0	35	1.15
49380721--49381085	190	1.9	185	81	5	428	30	19	23	26	1.98
49380907--49381518	114	5.4	113	78	4	559	31	19	23	25	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49380988--49381513	229	2.3	227	80	4	630	32	18	23	25	1.97
49386319--49387145	9	92.4	9	77	10	774	47	15	2	33	1.61
49386965--49387039	25	3.0	24	80	9	69	42	21	2	33	1.67
49387107--49387152	7	6.0	7	90	9	56	52	17	0	30	1.45
49392734--49392784	21	2.4	21	90	0	75	35	17	45	1	1.60
49393164--49393330	43	3.9	44	75	6	153	34	17	19	28	1.95
49393147--49393374	42	5.3	43	73	3	154	31	17	20	30	1.96
49393148--49393369	87	2.6	88	79	4	222	31	18	21	28	1.96
49395380--49395436	25	2.2	26	90	3	89	61	8	5	24	1.46
49402524--49402582	27	2.2	27	84	0	73	15	20	38	25	1.91
49403208--49403247	21	1.9	21	85	10	55	42	2	0	55	1.13
49403433--49403479	22	2.1	22	84	0	58	44	0	6	48	1.28
49404617--49404660	22	2.0	21	83	12	54	45	11	15	27	1.81
49404898--49405034	42	3.3	42	90	2	204	48	18	21	11	1.79
49441016--49441104	3	30.0	3	69	10	58	61	2	5	30	1.31
49441021--49441084	23	3.0	21	69	20	53	62	3	4	29	1.31
49441711--49441763	27	2.0	27	81	7	63	73	7	16	1	1.15
49441751--49441825	39	1.9	39	100	0	150	50	16	4	29	1.62
49442421--49442747	132	2.5	132	91	2	514	25	26	18	29	1.98
49442817--49443471	89	7.4	89	87	0	873	22	25	24	27	2.00
49448005--49448039	18	1.9	18	88	0	52	28	5	5	60	1.43
49464832--49465139	46	6.3	48	84	11	335	35	14	22	27	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49465103--49465285	37	5.0	37	93	1	316	37	16	21	24	1.94
49467087--49467191	6	18.0	6	83	13	123	81	1	16	0	0.77
49467090--49467181	7	13.4	7	81	11	93	82	2	15	0	0.76
49467924--49467964	16	2.7	15	85	7	64	43	21	2	31	1.66
49468232--49468895	100	6.7	100	90	1	965	32	22	20	24	1.98
49468232--49468895	299	2.2	299	90	1	1008	32	22	20	24	1.98
49468235--49468892	50	13.2	50	74	2	505	32	22	20	24	1.98
49469008--49469125	47	2.6	46	80	9	136	23	22	26	27	1.99
49470889--49470925	19	1.9	19	88	0	56	24	0	10	64	1.25
49471457--49471483	2	13.5	2	100	0	54	48	0	0	51	1.00
49475711--49475737	2	13.5	2	100	0	54	51	0	0	48	1.00
49484194--49484260	31	2.2	30	81	5	80	35	10	11	41	1.76
49497530--49497569	2	20.0	2	100	0	80	50	0	0	50	1.00
49510587--49510657	34	2.1	34	100	0	142	38	15	12	33	1.85
49516655--49516710	2	28.0	2	100	0	112	0	0	50	50	1.00
49520752--49520785	14	2.4	15	85	14	54	44	5	14	35	1.70
49528592--49528631	3	13.0	3	94	5	71	67	0	0	32	0.91
49528682--49528736	18	3.0	19	68	26	55	61	5	0	32	1.19
49528808--49528850	20	2.3	18	80	8	50	62	4	0	32	1.15
49529651--49529683	13	2.6	13	90	4	50	30	0	0	69	0.88
49531901--49531938	14	2.7	14	80	15	51	42	5	0	52	1.24
49536482--49536521	6	6.8	6	91	2	55	20	7	0	72	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49542358--49542417	29	2.1	28	81	9	68	41	0	5	53	1.23
49562372--49562444	37	2.0	37	88	0	110	49	6	2	41	1.44
49562386--49562446	17	3.4	18	71	11	54	47	4	3	44	1.41
49565471--49565574	52	2.0	52	100	0	208	26	15	19	38	1.91
49572393--49572426	16	2.1	16	94	0	59	11	26	20	41	1.87
49573957--49573994	20	1.9	20	88	0	58	50	5	0	44	1.24
49574641--49574714	15	4.9	15	69	27	59	52	4	0	43	1.20
49574829--49575250	230	1.8	229	89	1	657	44	6	9	38	1.64
49576112--49576144	16	1.9	18	88	11	52	54	0	0	45	0.99
49576227--49576292	27	2.4	28	80	12	73	28	1	19	50	1.57
49584722--49584789	21	3.3	21	91	2	102	25	2	29	42	1.69
49584722--49584774	7	7.6	7	95	0	97	28	1	28	41	1.67
49586278--49586557	140	2.0	140	97	0	524	27	15	22	35	1.93
49600992--49601404	120	3.4	121	93	4	687	42	2	5	49	1.41
49601117--49601158	15	2.9	15	82	10	52	47	0	0	52	1.00
49601237--49601288	15	3.6	15	80	12	56	44	0	1	53	1.11
49601166--49601332	39	4.2	39	66	20	103	40	3	6	49	1.46
49601322--49601354	16	1.9	18	88	11	52	48	3	6	42	1.43
49601366--49601407	15	2.7	16	82	14	52	45	0	2	52	1.13
49601357--49601398	15	2.9	15	82	10	52	47	0	0	52	1.00
49601341--49601659	159	2.0	157	95	1	575	47	5	3	43	1.40
49601512--49601546	18	2.0	17	88	5	52	45	0	0	54	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
49602193--49602218	5	5.2	5	100	0	52	80	0	0	19	0.71
49603057--49603158	25	4.1	25	87	6	145	23	29	19	27	1.98
49606582--49606623	23	2.0	22	86	13	61	42	0	2	54	1.13
49612106--49612159	27	2.0	27	85	7	74	29	1	0	68	1.00
49618681--49618963	126	2.3	125	88	3	417	28	15	22	32	1.95
49622120--49622178	29	2.0	29	83	3	73	45	15	15	23	1.84
49622987--49623017	13	2.4	13	94	0	53	41	0	6	51	1.27
49632542--49632599	28	2.1	28	93	0	98	31	29	17	22	1.96
49634217--49634266	20	2.7	18	72	22	50	48	4	4	44	1.40
49635790--49636299	255	2.0	255	99	0	1002	39	13	10	36	1.80

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