genome.fa.s4.2.7.7.80.10.50.1000.184.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  184  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)
57226174--57226467	43	6.8	43	76	9	226	25	15	26	32	1.96
57226217--57226467	129	1.9	129	86	3	353	24	15	27	32	1.96
57228360--57228409	22	2.2	24	82	13	61	42	0	30	28	1.56
57228661--57228698	16	2.3	16	95	4	67	15	0	26	57	1.38
57228715--57228804	18	5.2	18	69	10	80	23	1	12	63	1.35
57228677--57228786	50	2.2	50	91	0	175	20	2	17	59	1.50
57228753--57228804	12	4.3	12	82	0	50	25	1	7	65	1.30
57229116--57229247	62	2.1	61	88	4	194	25	6	20	47	1.74
57231121--57231189	26	2.6	27	81	6	79	27	8	13	50	1.70
57231115--57231389	97	2.8	97	92	0	444	26	6	18	48	1.72
57231225--57231286	26	2.4	27	83	5	74	29	8	11	51	1.66
57233294--57233318	3	8.3	3	100	0	50	0	32	0	68	0.90
57241446--57241490	22	2.0	23	86	4	65	4	6	24	64	1.37
57244175--57244205	9	3.4	9	95	0	53	51	19	0	29	1.47
57245744--57245782	9	4.1	9	83	9	51	0	15	10	74	1.07
57247310--57247348	14	2.8	14	80	0	51	35	10	12	41	1.77
57247888--57247957	16	4.4	16	87	0	104	30	28	4	37	1.76
57247986--57248059	38	1.9	39	94	2	132	16	2	28	52	1.57
57248040--57248064	13	1.9	13	100	0	50	12	0	48	40	1.40
57257645--57257670	12	2.2	12	100	0	52	38	38	15	7	1.76
57267227--57267278	25	2.1	25	96	0	95	34	3	5	55	1.42
57271140--57271184	22	2.0	23	86	4	65	28	2	4	64	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57284552--57284589	12	3.2	12	88	0	58	28	10	15	44	1.80
57299022--57299061	17	2.4	17	91	0	62	25	35	5	35	1.78
57299753--57299855	22	4.4	22	81	8	91	38	19	25	16	1.92
57299753--57299878	25	5.3	24	86	6	134	38	19	24	16	1.92
57300828--57300865	5	7.6	5	100	0	76	57	0	0	42	0.98
57300910--57300935	7	3.7	7	100	0	52	26	0	11	61	1.30
57301755--57301788	10	3.0	12	83	16	54	5	17	0	76	0.98
57301838--57301905	8	8.4	8	71	20	52	51	1	1	45	1.19
57305474--57305517	16	2.8	15	86	10	61	72	13	0	13	1.12
57305474--57305515	20	2.1	20	86	8	59	73	14	0	11	1.09
57307086--57307312	44	5.2	44	68	15	112	28	24	18	29	1.98
57307040--57307310	132	2.1	132	86	4	377	26	23	19	30	1.98
57307900--57308001	45	2.2	45	76	8	107	51	8	13	25	1.70
57328041--57328127	39	2.2	40	89	6	133	41	2	4	51	1.35
57330908--57330944	16	2.3	16	95	0	65	45	16	2	35	1.61
57333032--57333068	20	2.0	20	84	10	51	67	2	13	16	1.34
57340027--57340065	21	1.9	20	89	5	60	41	2	0	56	1.13
57342849--57342886	19	2.0	19	100	0	76	21	10	5	63	1.46
57342851--57342892	19	2.2	19	91	0	66	28	7	4	59	1.44
57346175--57346238	32	2.0	32	85	11	87	45	4	3	46	1.39
57348039--57348096	26	2.2	26	81	6	64	18	20	20	39	1.92
57348037--57348218	25	7.4	25	66	17	76	19	24	21	35	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57348085--57348230	73	2.0	73	81	10	174	19	26	21	32	1.97
57348110--57348292	25	7.4	25	72	8	106	20	25	21	32	1.97
57348632--57348695	23	2.7	24	80	7	69	53	1	1	43	1.19
57349145--57349178	16	2.0	18	88	11	54	50	0	20	29	1.49
57349582--57349676	3	31.7	3	100	0	190	33	0	0	66	0.92
57350034--57350129	39	2.5	39	80	6	108	22	23	26	27	2.00
57354274--57354312	21	1.9	21	84	5	53	51	2	0	46	1.14
57357464--57357496	11	3.1	11	95	4	59	84	0	9	6	0.76
57363635--57363762	39	3.3	38	80	15	156	61	1	3	33	1.21
57363722--57363746	11	2.3	11	100	0	50	52	0	8	40	1.31
57367731--57367764	3	11.3	3	93	0	59	70	0	29	0	0.87
57368995--57369044	20	2.5	20	77	9	57	56	2	0	42	1.11
57370449--57370482	12	2.8	12	86	0	50	64	0	17	17	1.29
57370681--57370730	12	4.2	12	81	0	55	50	0	8	42	1.32
57370684--57370730	18	2.6	18	83	6	60	48	0	8	42	1.33
57370612--57370712	2	52.0	2	75	9	66	48	2	3	44	1.36
57370756--57370872	17	6.9	18	80	11	54	59	5	3	31	1.35
57370762--57370876	3	39.0	3	80	3	135	60	4	2	32	1.30
57371835--57371870	5	7.2	5	93	0	63	77	0	2	19	0.88
57372443--57372712	48	5.5	48	71	6	193	20	22	24	32	1.98
57372359--57372747	98	4.0	98	89	1	521	22	21	23	32	1.98
57372400--57372663	50	5.4	50	72	7	234	21	20	23	33	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57386431--57386464	12	2.8	12	86	0	50	64	0	17	17	1.29
57386589--57386708	2	62.0	2	81	6	113	50	2	1	45	1.25
57397582--57397630	24	2.0	24	88	0	71	40	2	0	57	1.10
57397656--57397877	92	2.4	92	82	5	270	33	8	21	36	1.83
57407383--57407502	64	1.9	64	91	3	197	30	14	13	42	1.83
57414055--57414110	28	1.9	30	89	7	89	58	1	10	28	1.41
57415690--57415722	17	1.9	17	100	0	66	15	6	18	60	1.54
57422748--57423467	44	15.6	44	72	12	437	31	19	21	27	1.97
57422792--57423143	94	3.7	93	73	14	290	30	20	22	27	1.98
57422697--57423000	138	2.2	138	90	1	475	28	19	23	28	1.98
57422748--57423373	189	3.3	186	79	6	558	31	19	20	28	1.97
57423159--57423351	51	3.9	51	75	9	211	33	17	19	29	1.95
57423079--57423467	139	2.8	132	78	8	393	32	18	20	28	1.96
57422748--57423467	95	7.7	94	74	12	428	31	19	21	27	1.97
57429901--57429949	24	1.9	25	84	12	64	55	2	2	40	1.23
57434570--57434615	16	2.6	17	80	19	51	45	0	32	21	1.52
57434694--57434753	30	2.0	31	86	3	86	40	0	40	20	1.52
57435055--57435094	9	4.4	9	100	0	80	42	22	12	22	1.87
57435826--57435880	19	3.1	18	82	14	62	67	0	9	23	1.19
57436384--57436435	22	2.4	22	80	0	59	13	23	25	38	1.91
57436666--57436712	21	2.2	21	79	17	53	48	0	19	31	1.49
57455291--57455330	2	20.0	2	100	0	80	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57457589--57457646	30	2.0	31	86	10	86	55	6	8	29	1.56
57459846--57459870	12	2.1	12	100	0	50	84	8	8	0	0.79
57459873--57459920	21	2.2	21	82	10	53	68	4	27	0	1.07
57459894--57459929	17	2.0	17	89	10	54	72	0	27	0	0.85
57459847--57459920	28	2.8	26	78	8	71	71	5	20	2	1.18
57460608--57460646	21	1.9	20	89	5	60	35	0	12	51	1.40
57465320--57465355	17	2.0	18	89	10	56	72	0	25	2	0.98
57470136--57470205	28	2.5	28	77	13	81	48	2	0	48	1.16
57475867--57475917	25	2.0	25	96	0	93	29	5	15	49	1.68
57476293--57476481	58	3.2	58	76	10	161	50	14	13	20	1.77
57482643--57482668	2	13.0	2	100	0	52	50	0	0	50	1.00
57486100--57486169	34	2.0	35	86	2	97	51	5	4	38	1.45
57492120--57492155	14	2.7	13	91	4	54	19	0	33	47	1.50
57492121--57492164	12	3.4	13	87	6	54	20	0	38	40	1.53
57492218--57492328	34	3.2	35	82	5	127	39	0	15	45	1.46
57492230--57492342	34	3.4	33	85	6	140	40	0	12	46	1.41
57494202--57494391	56	3.6	54	81	11	227	26	20	28	24	1.99
57494202--57494428	49	4.5	50	79	8	192	27	20	27	24	1.99
57494199--57494428	99	2.3	102	78	6	252	28	20	26	23	1.99
57500882--57500920	18	2.2	17	86	13	53	33	0	20	46	1.51
57501025--57501053	8	3.6	8	100	0	58	24	13	27	34	1.93
57501140--57501215	23	3.3	23	94	0	134	21	21	25	32	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57503198--57503236	20	2.1	17	86	13	51	61	7	0	30	1.24
57505134--57505173	11	3.6	11	96	0	71	20	25	7	47	1.75
57507178--57507552	124	3.0	124	90	2	576	33	22	15	28	1.95
57516202--57516261	31	1.9	31	89	0	93	45	6	11	36	1.67
57517699--57517744	12	3.7	12	81	18	58	23	0	6	69	1.11
57517699--57517739	14	3.1	13	86	13	57	24	0	7	68	1.15
57521836--57521919	29	2.9	27	79	12	62	19	8	8	64	1.46
57521926--57521971	21	2.1	21	88	4	65	36	8	4	50	1.53
57521932--57521974	22	2.0	21	95	4	77	34	4	4	55	1.41
57522059--57522096	18	2.1	19	90	5	60	44	13	0	42	1.43

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