genome.fa.s4.2.7.7.80.10.50.1000.172.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  172  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)
53953009--53953583	229	2.5	229	89	3	851	30	18	22	27	1.98
53953535--53953621	41	2.1	41	82	4	104	18	21	27	32	1.97
53953009--53953583	114	5.0	114	89	1	823	30	18	22	27	1.98
53954327--53954357	14	2.1	15	94	5	55	29	0	32	38	1.57
53954093--53954832	320	2.3	320	97	1	1385	29	3	26	41	1.72
53954647--53954677	14	2.1	15	94	5	55	29	0	32	38	1.57
53954740--53954778	17	2.4	16	84	12	53	30	0	33	35	1.58
53954747--53954779	17	1.9	17	93	0	57	27	0	36	36	1.57
53955120--53955172	20	2.6	20	79	8	54	66	7	1	24	1.28
53955467--53955738	84	3.2	83	79	5	251	27	16	23	31	1.96
53958205--53958359	31	5.1	31	77	17	173	47	10	0	40	1.43
53958228--53958350	22	5.5	22	69	21	69	47	11	0	40	1.45
53958205--53958331	34	3.8	34	85	11	172	48	10	0	40	1.43
53958293--53958349	22	2.4	24	80	19	75	42	12	1	43	1.52
53958308--53958353	22	2.1	22	100	0	92	45	13	0	41	1.43
53958340--53958490	9	17.7	9	73	13	113	41	18	1	39	1.59
53958345--53958377	16	2.1	16	100	0	66	45	24	0	30	1.53
53958195--53958378	56	3.1	58	77	16	146	46	13	0	39	1.47
53958492--53958547	25	2.2	25	83	0	67	44	14	5	35	1.68
53958528--53958561	16	2.1	16	94	0	59	52	14	0	32	1.42
53964063--53964209	66	2.2	66	86	4	199	40	17	29	13	1.87
53964191--53964258	21	3.2	21	87	0	82	35	19	39	5	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53964228--53964268	21	2.0	21	100	0	82	31	19	43	4	1.72
53964622--53964976	43	8.3	43	74	4	259	23	19	29	26	1.98
53964622--53964854	129	1.8	129	81	3	290	22	16	31	29	1.96
53964642--53964915	86	3.2	86	86	1	334	25	17	31	25	1.97
53964899--53965043	43	3.4	43	75	2	130	28	30	19	21	1.97
53968820--53968851	16	1.9	17	93	6	57	50	0	0	50	1.00
53978724--53978821	50	2.0	50	81	4	117	39	14	15	30	1.87
53985025--53985074	17	2.9	17	82	8	57	72	2	0	26	0.96
53985050--53985080	5	6.0	5	92	7	53	77	0	0	22	0.77
53985041--53985079	16	2.4	16	87	8	53	79	0	0	20	0.73
53990296--53990396	31	3.3	31	73	8	107	52	3	3	39	1.39
53990699--53990868	85	2.0	85	96	0	313	18	22	18	39	1.92
53991964--53992008	22	2.0	22	100	0	90	28	17	13	40	1.88
53992459--53992493	18	2.0	18	88	5	54	54	5	20	20	1.64
53993445--53993473	14	2.1	14	93	6	51	13	0	3	82	0.79
53994793--53994928	40	3.5	39	77	9	125	33	27	16	22	1.96
53995895--53995926	3	10.7	3	100	0	64	65	0	0	34	0.93
53997758--53998014	27	9.5	27	80	0	271	18	18	21	41	1.91
53997758--53998025	81	3.3	80	83	3	329	19	17	22	41	1.90
53998640--53998686	24	1.9	24	86	4	67	27	34	0	38	1.57
54000941--54001195	27	9.5	26	82	6	260	21	16	20	41	1.90
54000951--54001195	54	4.6	52	84	7	294	21	16	20	42	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54005925--54005991	34	1.9	35	87	3	100	31	8	14	44	1.76
54007214--54007302	46	1.9	46	86	0	124	34	10	16	38	1.83
54015291--54015369	24	3.2	24	78	8	72	35	17	29	17	1.93
54017704--54017741	18	2.2	17	86	9	51	55	10	0	34	1.34
54024494--54024566	27	2.7	27	77	12	78	43	0	30	26	1.55
54024420--54024579	74	2.2	73	85	7	207	43	0	30	25	1.55
54026737--54026987	43	5.8	43	89	1	378	23	31	19	25	1.98
54026737--54027044	129	2.4	129	80	3	289	25	28	18	27	1.98
54027331--54027376	21	2.2	21	88	0	65	6	39	19	34	1.78
54027331--54027524	87	2.2	87	89	0	289	12	27	18	40	1.87
54028306--54028343	19	2.0	19	94	0	67	23	28	5	42	1.76
54031388--54031439	26	1.9	27	84	7	70	21	9	13	55	1.66
54035381--54035518	40	3.5	38	76	7	114	36	18	23	21	1.95
54035552--54035706	41	3.8	41	90	0	238	21	18	30	29	1.97
54036051--54036088	14	2.7	15	84	12	53	26	2	31	39	1.70
54037740--54037769	9	3.3	9	95	0	51	60	23	0	16	1.36
54039968--54039993	5	5.2	5	100	0	52	19	19	19	42	1.90
54040626--54040658	16	2.0	17	88	5	50	60	3	12	24	1.46
54041229--54041380	76	2.0	76	98	0	295	36	13	15	34	1.87
54043684--54043785	43	2.4	43	88	0	150	18	15	30	35	1.92
54046599--54046646	24	1.9	24	83	8	60	33	14	6	45	1.70
54050401--54050454	13	4.2	13	90	0	81	27	12	24	35	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54050391--54050454	26	2.5	26	81	0	83	29	12	20	37	1.89
54053635--54053683	20	2.5	19	77	6	53	63	6	14	16	1.49
54055303--54055348	23	2.0	23	100	0	92	34	8	13	43	1.74
54059042--54059103	31	2.0	31	84	3	81	45	9	3	41	1.53
54059502--54059543	16	2.6	16	92	0	66	42	7	2	47	1.43
54066424--54066462	14	2.8	14	96	0	69	30	23	10	35	1.88
54067737--54067798	21	3.0	21	87	0	88	43	17	19	19	1.88
54076872--54076923	24	2.2	24	89	0	77	55	9	1	32	1.43
54077425--54077475	20	2.5	21	78	15	61	33	5	0	60	1.21
54082038--54082096	23	2.4	24	77	11	66	16	3	15	64	1.42
54082041--54082088	23	2.1	24	88	7	73	18	4	18	58	1.55
54082048--54082096	23	2.1	23	88	7	73	18	2	18	61	1.45
54093296--54093600	161	1.9	160	86	3	434	46	10	27	15	1.78
54095210--54095255	23	2.0	23	83	8	58	23	4	30	41	1.74
54095909--54095958	18	2.6	19	84	6	57	54	12	0	34	1.38
54096228--54096282	26	2.1	26	89	0	83	27	25	7	40	1.82
54096244--54096287	21	2.2	20	83	4	52	29	20	6	43	1.78
54096527--54096584	25	2.2	25	87	6	80	39	0	1	58	1.08
54096607--54096660	20	2.8	18	72	22	56	29	1	5	62	1.28
54097789--54097822	14	2.4	14	85	14	52	64	8	14	11	1.49
54102094--54102127	14	2.4	14	85	14	52	64	8	14	11	1.49
54104557--54104615	29	2.0	29	81	12	68	37	0	3	59	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54104675--54104853	68	2.9	59	83	13	250	45	8	5	40	1.57
54104764--54104791	9	3.1	9	100	0	56	57	10	0	32	1.33
54104705--54104875	68	2.5	68	95	1	310	47	8	4	40	1.52
54104864--54104905	16	2.6	16	92	0	66	42	7	2	47	1.43
54104879--54104939	22	2.8	21	87	5	77	45	1	1	50	1.21
54106531--54106555	13	1.9	13	100	0	50	48	8	20	24	1.76
54109361--54109410	22	2.3	22	82	0	64	46	0	4	50	1.20
54123929--54124040	41	2.7	41	87	0	143	29	25	18	25	1.98
54124128--54124270	76	1.9	75	82	8	182	46	19	2	30	1.64
54124529--54124596	2	34.5	2	75	8	59	44	5	4	45	1.48
54131593--54131628	2	18.0	2	100	0	72	50	0	0	50	1.00
54132069--54132171	41	2.5	41	85	3	127	26	27	20	26	1.99
54132109--54132186	41	1.9	41	89	0	120	28	26	20	24	1.99
54139948--54140027	41	2.0	41	89	0	124	30	25	18	26	1.98
54139948--54140040	41	2.3	41	86	0	123	30	24	18	26	1.98
54140532--54140564	2	16.5	2	93	0	57	48	3	0	48	1.17
54143199--54143232	17	1.9	18	94	5	61	41	0	14	44	1.45
54143637--54143730	28	3.3	27	72	19	84	22	17	17	43	1.87
54154090--54154115	2	13.0	2	100	0	52	50	0	0	50	1.00
54154253--54154288	2	18.0	2	100	0	72	50	0	0	50	1.00
54166970--54167025	24	2.2	26	81	12	73	30	1	3	64	1.21
54169429--54169480	4	12.8	4	80	11	61	48	3	1	46	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54173136--54173423	51	5.7	50	80	3	326	28	15	26	28	1.96
54173136--54173417	102	2.8	102	91	0	431	28	15	26	28	1.96
54173143--54173462	102	3.1	102	87	1	293	30	14	26	28	1.95
54174531--54174561	15	2.1	15	100	0	62	29	0	25	45	1.54
54175559--54175634	29	2.6	28	77	8	80	25	7	1	65	1.27
54175686--54175807	29	4.3	29	72	19	87	28	4	4	62	1.34
54175687--54175813	28	4.6	25	74	15	92	28	4	3	62	1.33
54175687--54175813	57	2.3	54	83	12	161	28	4	3	62	1.33
54175732--54175868	75	1.9	72	83	4	175	28	5	5	61	1.39
54175695--54175923	26	8.8	26	73	12	143	27	6	6	60	1.45

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