genome.fa.s9.2.7.7.80.10.50.1000.105.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  105  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)
36246855--36247363	228	2.2	228	97	0	964	44	12	1	40	1.52
36247308--36247351	19	2.3	19	92	0	70	47	11	2	38	1.52
36247347--36247961	9	67.2	9	76	12	499	44	17	0	36	1.56
36246855--36247489	228	2.8	228	88	4	730	45	13	1	39	1.52
36247416--36247543	60	2.2	58	81	15	144	44	16	2	36	1.61
36247457--36247539	13	6.8	13	67	25	56	42	15	3	38	1.65
36247498--36247536	19	2.0	19	90	5	60	43	15	2	38	1.60
36247448--36247539	32	3.0	32	93	6	156	42	15	3	39	1.63
36253922--36254213	42	6.9	42	86	6	355	25	22	20	31	1.98
36253922--36254228	126	2.4	127	87	6	426	24	23	20	31	1.98
36254487--36254516	11	2.7	11	94	0	51	40	6	3	50	1.45
36255054--36255082	4	7.5	4	92	7	51	27	0	0	72	0.85
36263523--36263575	22	2.3	23	83	3	63	28	0	3	67	1.07
36264008--36264311	140	2.2	140	90	2	493	30	21	21	25	1.98
36264577--36264620	23	2.0	23	91	8	74	36	0	0	63	0.95
36264577--36264637	23	2.9	21	81	11	70	34	0	1	63	1.04
36271191--36271261	23	3.0	23	74	17	56	56	15	2	25	1.53
36272632--36272705	35	2.1	35	82	0	85	47	9	4	39	1.55
36272900--36272952	19	2.8	19	82	0	70	62	0	0	37	0.96
36273937--36273984	21	2.3	20	82	13	53	66	14	0	18	1.25
36283344--36283395	20	2.6	19	75	6	59	19	7	3	69	1.29
36286934--36287024	46	2.0	46	97	0	173	32	21	20	24	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
36289043--36289106	22	3.0	21	88	6	92	29	4	34	31	1.78
36290347--36290417	30	2.4	30	83	9	83	40	9	26	22	1.85
36293070--36293114	2	22.5	2	100	0	90	0	0	48	51	1.00
36293116--36293143	2	14.0	2	100	0	56	50	0	0	50	1.00
36294718--36294822	33	3.2	33	82	5	106	35	15	20	28	1.93
36298081--36298197	62	1.9	60	82	5	146	48	3	5	41	1.44
36299893--36299923	16	1.9	16	100	0	62	70	6	9	12	1.31
36304150--36304193	23	1.9	23	95	0	79	13	27	34	25	1.93
36316303--36316424	23	5.3	23	87	3	174	29	26	21	22	1.99
36316310--36316424	46	2.5	46	94	0	194	29	26	21	22	1.99
36316650--36316688	18	2.2	17	86	13	53	46	20	0	33	1.51
36328265--36328295	13	2.4	13	94	0	53	61	6	3	29	1.37
36338585--36338628	22	2.0	22	90	0	70	9	18	27	45	1.79
36338699--36338949	43	5.8	43	85	1	306	26	30	18	24	1.98
36338935--36338965	16	1.9	16	93	0	53	45	22	19	12	1.84
36343720--36343934	109	2.0	109	100	0	430	27	9	32	31	1.88
36344809--36344927	54	2.2	54	84	3	157	47	20	0	32	1.51
36345025--36345053	14	2.0	15	93	6	51	34	34	0	31	1.58
36345450--36345812	113	3.3	112	82	6	397	26	23	22	26	2.00
36345861--36346001	40	3.5	40	79	8	144	24	23	19	32	1.97
36348831--36348899	28	2.5	27	82	13	79	63	1	0	34	1.03
36348960--36348998	20	2.0	20	94	0	69	33	17	12	35	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
36349356--36349387	9	3.6	9	95	0	55	40	0	59	0	0.97
36350368--36350407	21	1.9	21	89	0	62	22	10	25	42	1.84
36353530--36353603	35	2.1	35	89	0	112	47	24	5	22	1.72
36354798--36354861	22	2.9	22	76	13	69	28	1	4	65	1.21
36356294--36356330	18	2.1	18	89	0	56	45	13	10	29	1.77
36356315--36356354	14	2.9	14	84	0	53	42	17	7	32	1.77
36366346--36366380	3	11.7	3	87	0	52	68	0	28	2	1.04
36368550--36368582	9	3.7	9	91	0	57	45	0	3	51	1.16
36375989--36376022	2	17.0	2	100	0	68	50	0	0	50	1.00
36376282--36376314	15	2.1	16	88	5	50	51	9	0	39	1.34
36379562--36379622	29	2.1	29	93	0	104	16	26	36	21	1.94
36382949--36382999	23	2.2	23	92	0	84	27	9	21	41	1.84
36384722--36384880	43	3.7	43	89	1	248	29	30	19	20	1.97
36384722--36384947	43	5.3	42	81	6	233	30	30	17	22	1.96
36384720--36384947	86	2.7	84	83	6	264	30	29	17	22	1.96
36384999--36385024	5	5.2	5	100	0	52	19	0	0	80	0.71
36386741--36386767	5	5.4	5	100	0	54	18	0	0	81	0.69
36389223--36389249	14	1.9	14	100	0	54	7	55	0	37	1.28
36389475--36389557	40	2.1	40	81	4	96	16	22	16	43	1.88
36390187--36390233	21	2.2	22	88	3	69	38	44	0	17	1.48
36391005--36391206	41	4.9	41	90	0	305	27	30	18	23	1.97
36391266--36391357	40	2.3	41	83	3	116	26	25	18	30	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
36391409--36391737	162	2.0	161	98	1	649	31	13	10	43	1.80
36394218--36394270	20	2.8	19	81	18	67	43	0	1	54	1.11
36394178--36394374	68	3.0	67	72	17	178	41	3	4	50	1.40
36394246--36394362	62	1.9	59	87	5	171	41	4	4	50	1.41
36398404--36398437	9	3.7	9	88	7	50	38	0	0	61	0.96
36402929--36402963	17	2.0	18	88	5	54	40	5	0	54	1.24
36407109--36407138	10	3.0	10	90	0	51	86	0	13	0	0.57
36407307--36407331	2	12.5	2	100	0	50	52	0	0	48	1.00
36408054--36408260	93	2.3	87	83	8	261	31	20	12	35	1.90
36408262--36408382	60	2.0	61	88	4	183	32	19	13	35	1.90
36408460--36408510	19	2.6	19	87	9	68	72	1	3	21	1.11
36408516--36408609	29	3.2	28	75	11	89	59	1	6	32	1.30
36408460--36408652	20	9.8	20	66	17	84	63	1	6	29	1.27
36408825--36408863	9	4.2	9	83	6	51	20	0	10	69	1.17
36408839--36408910	19	3.7	19	75	10	74	26	2	5	65	1.28
36408838--36408980	29	4.9	30	69	14	102	32	2	4	60	1.31
36408974--36408999	11	2.4	11	100	0	52	15	0	0	84	0.62
36409484--36409576	45	2.1	45	95	0	168	19	6	23	50	1.70
36413701--36413780	29	2.8	30	79	9	87	26	31	20	22	1.98
36413792--36413852	28	2.2	27	85	2	77	22	16	31	29	1.96
36426981--36427132	43	3.5	42	85	7	198	31	27	14	26	1.95
36431212--36431237	12	2.2	12	100	0	52	30	26	7	34	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
36432955--36433135	9	20.1	9	76	9	156	33	0	20	45	1.52
36432956--36433135	65	2.7	68	82	12	218	33	0	21	45	1.52
36432998--36433145	56	2.7	55	89	5	228	34	0	22	42	1.54
36433174--36433220	21	2.3	21	88	3	69	48	0	8	42	1.33
36433127--36433725	120	5.0	120	94	0	1000	46	2	8	42	1.49
36433294--36433340	21	2.3	21	88	3	69	48	0	8	42	1.33
36433414--36433460	21	2.3	21	88	3	69	48	0	8	42	1.33
36433534--36433580	21	2.3	21	88	3	69	48	0	8	42	1.33
36433655--36433701	21	2.3	21	88	3	69	48	0	8	42	1.33
36435310--36435340	15	2.1	15	93	0	53	0	29	6	64	1.18
36436201--36436290	7	12.6	7	78	9	92	48	35	0	15	1.45
36436184--36436290	22	4.9	21	78	12	101	49	33	0	16	1.46
36436338--36436390	7	7.7	7	78	4	63	43	33	0	22	1.54
36436338--36436391	20	2.7	20	94	2	90	42	33	0	24	1.55
36436523--36436737	115	1.9	114	85	8	301	31	21	17	30	1.96
36436515--36436760	115	2.1	114	81	8	277	32	22	16	28	1.96
36436748--36437086	155	2.2	155	88	1	491	29	22	17	30	1.97
36436887--36436998	40	2.8	40	80	0	125	25	23	22	28	1.99
36436793--36437136	155	2.2	155	87	3	478	28	21	18	31	1.97
36437940--36438292	42	8.4	42	85	3	401	30	22	20	25	1.98
36437962--36438292	125	2.6	124	84	7	375	31	22	20	25	1.98
36438710--36438749	21	1.9	21	94	0	71	0	42	20	37	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
36438734--36438761	12	2.3	12	100	0	56	0	42	17	39	1.50
36438717--36438781	33	2.0	33	93	0	112	3	40	20	36	1.68
36438746--36438814	21	3.3	21	85	0	93	4	40	18	36	1.71
36444369--36444416	25	1.9	25	87	8	71	33	0	25	41	1.55
36444369--36444420	9	6.0	9	78	17	65	32	0	25	42	1.55
36444406--36444481	33	2.4	31	80	10	98	42	0	10	47	1.38
36444513--36444739	90	2.5	89	97	0	355	44	8	6	40	1.61
36444561--36444636	27	2.9	27	94	2	127	46	10	3	39	1.57
36444651--36444726	27	2.9	27	94	2	127	46	10	3	39	1.57
36446621--36446649	11	2.7	11	94	5	51	68	0	3	27	1.05

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