genome.fa.s2.2.7.7.80.10.50.1000.158.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: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62769430

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   199   200   201   202   203   204   205   206   

This is table  158  of  206  ( 24623 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)
47766136--47766170	2	17.5	2	87	0	52	54	2	0	42	1.15
47768031--47768068	19	2.1	18	90	5	58	65	2	5	26	1.27
47771191--47771227	16	2.3	16	95	0	65	21	37	5	35	1.77
47776240--47776271	13	2.3	15	89	10	50	53	0	0	46	1.00
47776802--47777005	91	2.2	91	89	1	311	45	4	12	37	1.63
47781051--47781148	20	4.9	20	71	5	90	16	32	19	31	1.94
47781043--47781160	40	3.0	40	91	2	175	17	29	19	33	1.95
47781051--47781195	40	3.7	40	86	6	154	18	29	17	33	1.95
47783357--47783386	5	6.0	5	100	0	60	40	0	20	40	1.52
47783871--47783974	29	3.6	28	67	12	77	33	16	26	23	1.95
47783856--47783990	57	2.4	57	88	0	198	33	16	25	25	1.96
47783852--47784029	28	6.3	28	67	7	83	29	16	26	27	1.97
47783985--47784061	28	2.7	27	78	11	82	25	12	32	28	1.93
47786181--47786260	27	3.0	27	90	3	117	32	15	26	26	1.95
47786222--47786448	107	2.1	107	94	0	393	37	17	23	22	1.94
47786264--47786444	53	3.4	52	75	15	181	39	17	23	19	1.92
47786234--47786404	54	3.2	53	73	17	190	39	15	24	20	1.92
47786504--47786595	27	3.4	27	75	0	76	36	9	28	25	1.87
47789008--47789105	22	5.0	18	76	22	83	57	0	2	40	1.10
47789001--47789078	21	3.9	21	82	11	76	58	0	1	39	1.06
47789023--47789139	11	11.4	11	74	19	101	58	0	2	38	1.12
47789033--47789087	28	2.0	27	96	3	101	58	0	0	41	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47789035--47789152	41	3.0	38	82	10	141	61	0	1	37	1.07
47798211--47798490	96	2.9	95	84	3	330	36	2	18	43	1.63
47798523--47798939	126	3.3	126	91	0	665	32	18	21	27	1.97
47803399--47803452	11	4.9	11	78	15	58	40	1	31	25	1.66
47808539--47808831	35	8.3	35	76	3	255	29	5	30	34	1.80
47814755--47814804	21	2.4	21	89	0	73	32	28	10	30	1.89
47816079--47816138	27	2.2	27	87	0	84	13	18	36	31	1.89
47817084--47817114	6	5.2	6	92	0	53	67	3	16	12	1.35
47817078--47817114	12	3.1	12	88	0	56	64	5	16	13	1.45
47818424--47818511	24	3.7	24	73	8	81	40	22	13	22	1.89
47822976--47823048	36	2.0	36	100	0	146	31	13	21	32	1.93
47825639--47825671	2	16.5	2	100	0	66	48	0	0	51	1.00
47829970--47830008	18	2.2	18	100	0	78	30	5	28	35	1.79
47830552--47830603	16	3.2	16	94	0	86	28	0	36	34	1.58
47830584--47830678	45	2.1	44	88	1	136	32	6	27	33	1.82
47842570--47842741	48	3.5	48	73	6	166	20	22	23	33	1.98
47842486--47842873	98	4.0	98	85	1	483	22	20	23	32	1.98
47842527--47842790	50	5.4	50	69	7	198	22	19	24	33	1.97
47855026--47855061	5	7.2	5	100	0	72	80	0	0	19	0.71
47855801--47855830	7	4.4	7	95	4	53	46	13	0	40	1.43
47859194--47859248	3	19.0	3	78	14	53	69	0	0	30	0.89
47859193--47859248	15	3.4	17	78	14	64	67	0	0	32	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47859202--47859246	23	1.9	24	86	13	67	71	0	0	28	0.87
47859452--47859490	19	2.0	21	85	10	55	69	5	10	15	1.34
47859683--47859852	21	8.5	21	89	8	266	37	13	13	35	1.84
47859696--47859852	61	2.7	57	92	7	246	38	14	13	34	1.85
47859683--47859852	78	2.1	80	93	4	290	37	13	13	35	1.84
47860222--47860312	42	2.2	42	95	0	164	48	8	15	27	1.74
47861260--47861332	20	3.6	20	71	15	60	28	5	2	63	1.31
47861301--47861392	30	3.1	30	79	13	93	34	3	1	60	1.20
47861371--47861502	19	6.8	19	70	17	58	34	2	3	59	1.28
47861455--47861503	18	2.5	19	83	12	64	32	0	2	65	1.04
47864005--47864126	43	2.8	43	78	11	115	20	17	27	34	1.95
47874895--47875236	50	6.7	50	83	5	339	23	28	20	27	1.99
47885484--47885521	14	2.7	15	88	8	53	42	5	13	39	1.66
47885603--47885674	36	2.0	36	84	10	94	36	5	4	54	1.43
47888681--47888716	16	2.2	16	90	0	54	52	2	33	11	1.51
47895979--47896020	18	2.3	19	80	12	52	7	14	11	66	1.43
47919547--47919584	14	2.7	14	84	11	51	47	0	5	47	1.24
47919553--47919619	34	1.9	35	85	8	93	38	2	7	50	1.46
47919911--47919982	37	1.9	37	100	0	144	40	15	5	38	1.70
47921253--47921358	44	2.4	44	91	1	167	43	30	6	19	1.77
47921936--47921968	14	2.4	14	94	0	57	15	9	60	15	1.58
47925305--47925360	21	2.6	20	81	18	60	69	3	0	26	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47929845--47929915	25	3.0	23	81	4	70	39	18	21	21	1.93
47934871--47934922	12	4.3	12	78	7	52	44	21	1	32	1.63
47936520--47936553	17	2.0	17	88	0	50	41	32	8	17	1.80
47937408--47937451	23	2.0	21	83	16	54	36	0	20	43	1.52
47940805--47940858	24	2.2	24	83	6	65	55	5	3	35	1.41
47943006--47943035	15	2.0	15	93	0	51	23	0	13	63	1.29
47950832--47950970	41	3.4	41	86	0	179	33	25	22	18	1.97
47954186--47954228	20	2.2	20	87	8	61	16	20	2	60	1.46
47954399--47954578	50	3.6	49	80	4	175	22	27	21	27	1.99
47961626--47961663	15	2.5	15	95	0	67	55	0	23	21	1.44
47961847--47961884	15	2.5	15	95	0	67	55	0	23	21	1.44
47962364--47962404	18	2.3	18	87	8	57	48	12	12	26	1.75
47965373--47965472	46	2.2	46	84	8	134	37	24	12	27	1.90
47970434--47970472	15	2.6	15	100	0	78	30	17	7	43	1.77
47971336--47971372	18	2.0	19	89	5	58	32	16	5	45	1.70
47981566--47981610	16	2.7	16	89	6	63	40	0	0	60	0.97
47981594--47981666	11	6.3	11	73	16	58	35	1	0	63	1.04
47982189--47982250	6	10.3	6	73	13	56	45	3	32	19	1.66
47982204--47982256	18	2.9	18	76	15	56	43	3	32	20	1.70
47986035--47986174	75	1.9	74	98	1	271	39	19	6	35	1.77
47995637--47995879	50	4.8	50	77	9	199	23	25	21	28	1.99
47997594--47997639	22	2.0	22	83	4	56	50	10	15	23	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48002833--48002942	56	2.0	56	92	0	184	38	16	12	32	1.86
48007909--48007934	2	13.0	2	100	0	52	50	0	0	50	1.00
48010447--48010476	7	4.4	7	95	4	53	73	0	0	26	0.84
48014695--48014768	36	2.1	36	89	5	114	24	22	13	39	1.90
48019183--48019628	223	2.0	223	95	0	804	32	24	12	29	1.92
48020633--48020942	154	2.0	154	100	0	620	42	15	13	29	1.85
48021887--48021930	20	2.3	18	85	14	70	31	0	9	59	1.29
48022020--48022052	13	2.3	15	90	10	52	51	0	0	48	1.00
48022185--48022251	27	2.5	27	92	4	109	23	1	11	62	1.37
48024251--48024430	41	4.4	40	87	2	218	48	7	24	18	1.74
48024251--48024430	81	2.2	81	87	2	245	48	7	24	18	1.74
48040371--48042111	597	2.8	596	85	6	1959	31	11	21	35	1.89
48045233--48045280	15	3.5	14	81	18	57	27	0	8	64	1.22
48045254--48045286	15	2.1	16	94	5	59	27	0	6	66	1.15
48047583--48047740	78	2.0	78	97	0	298	41	18	3	36	1.68
48051790--48051832	23	2.0	23	86	9	63	39	0	16	44	1.48
48054309--48054348	20	2.0	20	90	0	62	47	7	5	40	1.54
48054924--48055127	107	1.9	108	84	3	277	35	14	14	35	1.86
48056995--48057027	17	1.9	17	93	0	57	48	0	6	45	1.27
48056989--48057040	17	2.8	18	77	14	52	50	0	3	46	1.20
48075429--48075582	79	1.9	79	96	0	281	47	22	5	24	1.72
48080959--48081000	14	3.0	14	79	6	50	11	7	4	76	1.15
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48083755--48083788	17	2.0	17	88	0	50	50	5	14	29	1.67
48090203--48090313	55	2.0	55	98	0	213	38	1	17	42	1.60
48099361--48099410	18	2.5	20	87	9	68	74	2	20	4	1.08
48103339--48103364	13	2.0	13	100	0	52	38	0	23	38	1.55
48108710--48108785	38	2.0	38	97	0	143	53	25	5	15	1.62
48109446--48109517	27	2.7	27	80	0	90	25	33	31	9	1.88
48109593--48109625	17	1.9	17	93	0	57	75	6	9	9	1.18
48109831--48109867	13	2.8	13	100	0	74	29	0	13	56	1.37
48110101--48110138	13	2.9	13	81	11	51	28	0	0	71	0.87
48110104--48110139	16	2.1	16	90	10	54	27	0	0	72	0.85

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   199   200   201   202   203   204   205   206