genome.fa.s20.2.7.7.80.10.50.1000.12.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: D07
Parameters: 2 7 7 80 10 50 1000
Length:  58101237

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   

This is table  12  of  199  ( 23844 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)
3924488--3924600	37	3.1	37	94	1	192	32	4	15	47	1.65
3924500--3924594	17	5.2	17	65	14	55	33	3	13	49	1.58
3924601--3924708	9	11.6	9	86	7	153	22	9	32	36	1.86
3924814--3924879	29	2.3	27	78	16	71	28	12	27	31	1.92
3925098--3925216	49	2.4	49	94	1	204	43	10	11	34	1.75
3925144--3925326	64	2.9	63	78	13	205	48	9	8	33	1.66
3933253--3933310	30	1.9	30	85	0	80	43	0	24	32	1.55
3933522--3933553	13	2.5	13	94	0	55	31	0	12	56	1.37
3933648--3933889	50	4.7	50	86	4	297	26	24	29	19	1.99
3933648--3933897	100	2.4	103	88	6	364	26	24	29	20	1.99
3935703--3935737	17	2.0	18	88	5	54	17	2	2	77	1.02
3936965--3937012	21	2.3	20	80	13	53	20	39	20	18	1.92
3937008--3937047	21	1.9	21	84	0	53	22	40	15	22	1.91
3937348--3937439	42	2.2	42	82	0	103	17	31	33	17	1.93
3938384--3938460	33	2.3	32	84	6	100	24	23	19	32	1.97
3938405--3938670	105	2.5	105	88	2	383	28	22	15	34	1.94
3945547--3945579	16	2.1	16	88	5	50	51	12	9	27	1.69
3945616--3945660	15	2.9	15	80	3	54	60	24	0	15	1.36
3945991--3946059	18	3.8	19	69	19	58	57	0	0	42	0.98
3948619--3948688	22	3.2	21	78	8	59	68	7	12	11	1.38
3949591--3949636	22	2.0	23	83	4	58	47	4	2	45	1.34
3967587--3967649	31	2.0	31	100	0	126	44	12	9	33	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3969573--3969618	19	2.4	19	85	0	65	65	2	4	28	1.23
3969824--3969893	15	5.0	14	75	20	58	38	1	0	60	1.06
3977009--3977056	24	2.0	24	95	0	87	41	6	0	52	1.27
3977266--3977305	21	2.0	20	85	5	53	37	2	0	60	1.11
3979802--3979841	15	2.9	15	89	10	59	40	15	5	40	1.68
3979941--3979992	16	3.2	16	97	0	95	36	0	34	28	1.58
3980072--3980110	19	2.1	19	100	0	78	58	5	15	20	1.55
3980233--3980274	15	2.9	15	82	10	52	52	0	0	47	1.00
3984195--3984245	20	2.5	21	90	3	77	54	0	1	43	1.11
3984424--3984464	21	2.0	21	90	0	64	26	17	19	36	1.94
3984618--3984668	20	2.5	21	90	3	77	54	0	1	43	1.11
3984750--3984809	27	2.2	26	77	13	68	65	1	1	31	1.13
3984743--3984783	19	2.1	20	86	4	57	63	2	4	29	1.28
3985755--3985802	10	4.9	10	76	2	53	66	2	6	25	1.26
3991777--3991867	45	2.0	44	87	2	128	54	3	4	37	1.37
3994883--3994921	15	2.4	16	83	12	53	53	5	7	33	1.51
4004136--4004175	21	1.9	21	90	10	64	22	10	10	57	1.61
4010134--4010219	39	2.2	39	89	0	127	32	19	16	31	1.94
4016384--4016434	5	10.2	5	77	8	50	62	1	0	35	1.06
4016386--4016426	20	2.0	21	90	4	66	65	2	0	31	1.05
4016376--4016434	20	2.6	23	74	20	61	61	1	0	37	1.07
4020886--4020931	16	2.7	17	90	6	67	60	2	0	36	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4021340--4021385	23	2.0	23	83	8	58	17	13	0	69	1.19
4029097--4029142	24	1.9	24	86	8	67	67	15	13	4	1.38
4034955--4035104	44	3.4	44	89	0	228	30	19	18	32	1.95
4037720--4037768	25	2.0	25	88	8	73	53	0	2	44	1.12
4037942--4038013	33	2.3	30	82	15	101	30	11	5	52	1.59
4041396--4041599	41	5.0	39	83	9	196	28	19	24	26	1.99
4041414--4041599	82	2.3	81	83	7	216	27	19	25	26	1.99
4048660--4048707	17	2.9	17	81	3	53	35	2	0	62	1.07
4049308--4049339	10	3.2	10	95	0	55	78	0	15	6	0.95
4052024--4052063	20	2.0	20	85	0	53	32	12	12	42	1.80
4052011--4052076	35	1.9	34	87	3	96	33	10	13	42	1.79
4053215--4053261	18	2.6	18	89	3	76	40	0	57	2	1.11
4053215--4053267	18	2.9	17	88	5	70	43	0	54	1	1.11
4063017--4063065	22	2.3	22	86	10	66	12	22	2	63	1.39
4066345--4066479	40	3.4	39	81	9	134	40	22	17	19	1.91
4066519--4066714	41	4.8	41	92	0	311	19	20	26	32	1.97
4067285--4067316	15	2.1	15	94	0	55	25	0	34	40	1.56
4067960--4067992	15	2.3	15	89	5	50	60	0	0	39	0.97
4068035--4068097	21	3.0	21	77	11	65	23	0	41	34	1.55
4068183--4068281	50	2.0	50	89	0	153	23	2	32	42	1.65
4078562--4078687	40	3.0	41	87	9	177	33	1	0	65	1.03
4078634--4078659	11	2.4	11	100	0	52	38	0	0	61	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4078605--4078660	29	1.9	29	85	7	78	33	1	0	64	1.04
4079175--4079386	90	2.4	90	95	0	388	25	15	24	34	1.95
4079135--4079423	135	2.1	134	81	8	345	25	14	25	34	1.94
4079141--4079386	45	5.5	45	81	10	288	26	15	24	34	1.95
4083429--4083490	29	2.1	29	96	0	115	54	12	8	24	1.64
4085710--4085749	3	13.3	3	100	0	80	0	32	0	67	0.91
4092036--4092093	27	2.1	28	96	3	109	24	0	0	75	0.80
4092052--4092128	38	2.1	38	87	7	113	33	1	1	63	1.11
4094137--4094165	15	1.9	15	100	0	58	58	6	6	27	1.50
4094266--4094298	16	2.1	16	94	0	57	36	3	36	24	1.71
4094278--4094386	45	2.6	43	77	10	109	35	5	27	31	1.80
4094510--4094553	16	2.8	16	82	10	54	50	2	0	47	1.13
4094515--4094927	120	3.4	120	95	0	718	50	5	1	42	1.35
4094631--4094682	15	3.6	15	80	12	56	53	1	0	44	1.11
4094968--4095109	43	3.2	42	70	19	117	48	2	2	46	1.28
4094934--4095149	91	2.4	90	86	6	292	46	4	3	45	1.38
4101054--4101107	23	2.3	24	75	15	60	62	3	1	31	1.23
4101345--4101393	16	3.2	16	66	16	50	51	4	0	44	1.20
4101596--4101621	6	4.3	6	100	0	52	65	0	0	34	0.93
4102429--4102515	44	2.0	44	93	0	147	50	10	9	29	1.67
4102433--4102526	44	2.1	44	88	0	134	53	9	9	27	1.65
4117986--4118105	35	3.5	36	69	16	103	36	0	7	55	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4117982--4118120	65	2.1	65	92	6	228	38	0	6	55	1.26
4118185--4118228	23	2.0	23	86	4	63	18	9	2	70	1.24
4121790--4121825	17	2.0	19	89	10	58	52	0	5	41	1.24
4122569--4124057	512	2.9	512	99	0	2955	31	22	12	32	1.92
4133716--4133770	26	2.1	26	82	0	65	45	1	1	50	1.22
4135744--4135805	30	2.0	31	87	9	92	54	3	0	41	1.16
4138152--4138198	21	2.2	22	92	3	78	21	38	19	21	1.94
4152128--4152152	10	2.5	10	100	0	50	16	0	0	84	0.63
4152772--4152876	52	2.0	53	96	1	194	32	8	1	57	1.40
4152979--4153026	10	4.6	10	82	10	60	35	2	2	60	1.20
4152984--4153025	22	1.9	22	90	0	66	35	2	2	59	1.23
4152960--4153026	32	2.1	33	86	8	93	35	2	1	59	1.22
4152979--4153033	22	2.6	21	77	11	58	38	1	1	58	1.20
4162872--4162976	53	2.0	53	96	0	192	32	31	7	28	1.85
4174047--4174099	20	2.5	21	72	9	54	41	1	1	54	1.22
4175453--4175490	17	2.2	17	90	0	58	50	10	7	31	1.66
4176207--4176233	13	2.1	13	100	0	54	44	0	0	55	0.99
4184867--4184894	3	9.3	3	100	0	56	64	0	0	35	0.94
4200294--4200352	30	1.9	30	89	3	91	37	0	10	52	1.35
4200602--4200639	16	2.4	16	83	12	51	52	0	0	47	1.00
4200609--4200642	17	2.1	17	94	5	61	47	0	0	52	1.00
4200881--4200942	31	2.0	31	81	6	72	46	3	6	43	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4202072--4202134	30	2.1	30	96	0	117	23	3	15	57	1.53
4207369--4207413	17	2.6	17	76	13	56	28	8	22	40	1.84
4208070--4208109	15	2.7	15	100	0	80	30	25	32	12	1.92
4210957--4211006	19	2.6	19	87	9	66	6	10	10	74	1.23
4225484--4225533	24	2.1	24	100	0	100	52	0	4	44	1.20
4226357--4226398	16	2.4	18	80	7	52	47	14	16	21	1.82
4226683--4226717	18	2.0	17	88	5	52	54	0	0	45	0.99
4226564--4226886	157	2.0	160	93	3	553	43	3	4	47	1.40
4226820--4226861	15	2.7	16	82	14	52	52	2	0	45	1.13
4226829--4226870	15	2.9	15	82	10	52	52	0	0	47	1.00

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