genome.fa.s9.2.7.7.80.10.50.1000.183.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: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  70713020

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   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   

This is table  183  of  226  ( 27023 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)
58485452--58485528	38	2.0	38	92	0	127	28	38	2	29	1.70
58488164--58488218	10	5.6	10	75	12	51	60	1	3	34	1.25
58488154--58488268	29	4.0	28	75	15	92	57	0	6	34	1.32
58488563--58488610	20	2.5	19	83	9	62	56	0	4	39	1.19
58490252--58490934	50	13.7	50	70	5	394	23	20	24	32	1.98
58490196--58490946	100	7.5	100	82	3	730	23	21	23	32	1.98
58490252--58490946	200	3.5	200	86	1	811	23	20	24	32	1.98
58490984--58491351	142	2.6	142	91	0	592	27	19	18	33	1.96
58497849--58497896	20	2.5	19	83	9	62	56	0	4	39	1.19
58503985--58504036	24	2.2	24	89	0	77	34	3	7	53	1.48
58507442--58507466	7	3.6	7	100	0	50	16	0	0	84	0.63
58507628--58507670	3	14.3	3	100	0	86	32	0	0	67	0.91
58508089--58508177	47	1.9	47	93	2	153	22	37	2	38	1.67
58509015--58509241	118	1.9	118	100	0	454	29	8	18	43	1.80
58517571--58518027	119	3.9	115	77	9	397	30	13	17	39	1.87
58521330--58521364	11	3.1	11	87	4	52	60	0	0	40	0.97
58525241--58525308	14	4.4	15	72	24	52	44	0	2	52	1.16
58525272--58525313	14	2.9	15	79	10	52	50	0	0	50	1.00
58525326--58525362	16	2.3	16	86	13	58	40	0	0	59	0.97
58525366--58525420	24	2.1	28	80	16	73	60	0	0	40	0.97
58525369--58525433	25	2.6	25	81	11	64	55	0	0	44	0.99
58528134--58528312	63	2.8	63	78	6	184	36	29	7	26	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
58533161--58533242	27	3.0	27	66	7	67	39	12	21	26	1.89
58533157--58533260	54	1.9	53	82	5	129	39	13	22	25	1.90
58554287--58554312	9	2.9	9	100	0	52	46	0	0	53	1.00
58564407--58564481	37	2.0	37	97	0	141	33	18	6	41	1.77
58572638--58572800	78	2.1	78	84	2	211	17	38	4	39	1.71
58573455--58573485	13	2.4	13	88	0	53	48	0	9	41	1.36
58574588--58574637	25	2.0	25	88	3	75	26	4	6	64	1.35
58575278--58575347	35	2.0	35	97	0	131	45	12	5	35	1.66
58581608--58581670	22	2.8	23	76	9	67	19	25	20	34	1.96
58581855--58581912	20	2.9	20	76	0	62	31	6	20	41	1.79
58588961--58589019	23	2.5	23	81	10	75	18	20	22	38	1.93
58589234--58589291	20	2.9	20	76	0	62	31	6	20	41	1.79
58595697--58595730	3	11.0	3	93	6	59	64	0	0	35	0.94
58599486--58599609	64	1.9	64	83	6	162	36	22	20	20	1.95
58603059--58603109	21	2.4	22	76	3	59	17	27	37	17	1.93
58603829--58603862	16	2.1	16	88	0	50	82	0	17	0	0.67
58604800--58604826	5	5.4	5	100	0	54	59	0	0	40	0.98
58605452--58605492	18	2.3	18	87	8	57	60	31	4	2	1.30
58615929--58615963	17	2.1	17	89	5	54	68	0	0	31	0.90
58616163--58616208	17	2.8	16	80	6	56	50	0	2	47	1.13
58616222--58616275	25	2.2	25	80	12	58	55	3	0	40	1.17
58616235--58616273	13	3.2	13	82	10	55	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
58616358--58616418	18	3.3	18	77	11	70	50	0	0	49	1.00
58619677--58619723	22	2.2	22	78	17	55	29	6	2	61	1.32
58628071--58628129	22	2.7	22	82	10	75	44	0	30	25	1.55
58628938--58628972	18	1.9	18	94	0	61	48	42	0	8	1.33
58629948--58629989	20	2.1	20	82	8	50	26	7	0	66	1.17
58631405--58631461	30	1.9	29	82	3	69	47	0	33	19	1.50
58631674--58631710	9	4.1	9	85	0	56	29	10	10	48	1.72
58635082--58635126	23	2.0	22	86	8	63	28	2	8	60	1.39
58644369--58644455	27	3.2	26	86	3	120	42	9	21	26	1.83
58648579--58648635	4	14.2	4	96	0	105	26	0	22	50	1.49
58649726--58649768	22	2.0	22	100	0	86	23	25	13	37	1.92
58653768--58653814	21	2.2	21	88	0	67	25	23	36	14	1.93
58654418--58654442	13	1.9	13	100	0	50	68	0	8	24	1.16
58654510--58654544	18	1.9	18	94	0	61	11	11	5	71	1.30
58660224--58660267	21	2.0	21	82	8	52	11	20	4	63	1.44
58662657--58662855	100	2.0	100	97	0	380	36	19	12	31	1.89
58663821--58663889	24	2.9	24	84	0	93	47	8	4	39	1.54
58666148--58666247	24	4.2	24	88	0	137	51	6	3	40	1.42
58666192--58666235	14	3.4	14	76	23	60	52	9	0	38	1.33
58666449--58666591	49	2.9	49	87	4	182	37	17	13	31	1.88
58666960--58667013	22	2.5	21	77	11	56	70	3	22	3	1.19
58667534--58667564	15	2.1	15	100	0	62	12	12	12	61	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
58672869--58673125	43	6.0	43	78	4	234	32	18	19	29	1.96
58672895--58673125	85	2.7	85	82	4	270	30	19	20	29	1.97
58673059--58673163	42	2.5	42	84	3	122	27	25	20	25	1.99
58676455--58676501	24	1.9	25	86	4	69	65	6	6	21	1.38
58676491--58676524	6	5.7	6	92	0	59	82	2	0	14	0.79
58676447--58676510	24	2.5	24	77	7	65	68	6	4	20	1.30
58687656--58687820	23	7.2	23	78	2	134	18	14	25	41	1.89
58687656--58687820	69	2.4	69	81	0	186	18	14	25	41	1.89
58697148--58697200	17	3.4	17	65	20	51	62	13	5	18	1.50
58697149--58697209	30	2.0	30	100	0	122	60	13	9	16	1.58
58697155--58697226	30	2.4	30	86	4	92	63	9	9	16	1.50
58698822--58698889	11	6.2	11	85	11	86	23	33	1	41	1.64
58700696--58700738	18	2.4	18	88	0	59	18	27	9	44	1.80
58700979--58701037	21	2.8	21	79	5	66	30	47	16	5	1.69
58701165--58701245	30	2.7	28	75	18	81	43	8	3	44	1.52
58704425--58705093	126	5.3	126	93	0	1140	26	22	18	32	1.97
58705115--58705348	95	2.4	96	89	1	335	39	19	3	37	1.69
58705115--58705394	95	2.9	95	82	4	278	41	18	3	36	1.68
58706749--58706779	16	1.9	16	93	0	53	19	6	16	58	1.59
58710236--58710377	68	2.1	68	97	0	266	39	7	17	35	1.79
58711001--58711044	13	3.4	13	78	12	54	34	2	22	40	1.67
58714889--58715026	40	3.5	38	73	8	109	27	18	21	31	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
58716996--58717035	2	20.0	2	100	0	80	50	0	0	50	1.00
58717289--58717334	23	2.0	23	100	0	92	39	8	17	34	1.80
58717564--58717679	58	2.0	58	94	0	205	34	17	11	37	1.85
58721638--58721734	48	2.0	48	100	0	194	26	14	12	46	1.80
58735940--58735964	12	2.1	12	100	0	50	24	36	24	16	1.94
58736121--58736223	27	3.8	27	93	0	161	40	27	8	23	1.84
58736121--58736223	18	5.7	18	91	0	143	40	27	8	23	1.84
58736121--58736206	9	9.6	9	93	0	145	38	27	10	23	1.87
58738068--58738094	7	3.9	7	100	0	54	59	0	0	40	0.98
58739880--58739920	20	2.0	20	100	0	82	36	14	4	43	1.67
58742979--58743037	28	2.1	28	93	0	100	27	20	28	23	1.99
58743136--58743185	26	1.9	26	87	0	73	42	20	20	18	1.90
58744275--58744321	19	2.4	18	80	19	51	72	2	14	10	1.21
58746077--58746142	25	2.6	25	81	9	89	25	21	24	28	1.99
58747881--58747951	36	2.0	35	83	10	90	36	2	5	54	1.38
58748555--58748599	21	2.1	21	84	8	56	6	15	2	75	1.11
58749213--58749250	20	1.9	20	88	0	58	50	0	10	39	1.37
58749005--58749427	154	2.8	147	84	8	541	42	4	9	43	1.56
58749005--58749493	147	3.3	145	81	11	519	43	4	8	43	1.55
58749434--58749480	24	2.1	22	84	11	60	44	4	4	46	1.42
58749004--58749493	148	3.3	146	80	12	507	43	4	8	43	1.55
58749415--58749492	21	3.7	21	74	14	61	50	5	6	38	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
58750451--58750476	11	2.4	11	100	0	52	42	0	7	50	1.31
58750769--58750806	3	12.7	3	100	0	76	68	0	0	31	0.90
58752099--58752142	19	2.3	18	81	11	52	15	6	6	70	1.31
58752778--58752836	30	2.0	30	100	0	118	16	25	23	33	1.96
58754732--58754764	16	2.1	16	94	0	57	36	21	12	30	1.90
58762082--58762158	34	2.2	35	82	11	88	67	1	24	6	1.22
58763135--58763431	42	7.1	43	87	2	347	23	18	20	37	1.94
58763135--58763431	84	3.5	84	84	0	387	23	18	20	37	1.94
58763135--58763431	126	2.4	126	86	2	409	23	18	20	37	1.94
58763438--58763468	16	1.9	16	100	0	62	19	19	9	51	1.74

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   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226