genome.fa.s4.2.7.7.80.10.50.1000.186.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  186  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)
57905932--57906049	53	2.2	53	87	0	182	27	11	3	58	1.48
57905959--57906041	26	3.2	26	66	10	60	30	9	3	56	1.48
57913740--57913832	41	2.2	42	83	5	109	25	15	24	34	1.94
57913822--57914020	43	4.7	43	85	0	229	24	20	29	25	1.99
57914826--57915587	111	6.8	110	78	7	680	32	19	16	31	1.94
57914832--57915587	225	3.4	219	81	6	776	32	19	16	30	1.94
57914861--57915597	333	2.2	331	81	8	862	32	18	16	32	1.93
57916071--57916155	11	8.5	11	73	21	80	55	0	1	43	1.07
57916074--57916155	10	8.3	10	75	20	66	56	0	1	42	1.07
57916071--57916151	30	2.8	30	83	14	107	56	0	1	41	1.07
57916105--57916137	16	2.0	17	88	5	50	63	0	0	36	0.95
57917434--57917468	18	1.9	18	88	11	54	62	0	2	34	1.10
57919015--57919117	14	7.3	13	70	14	62	29	5	3	61	1.37
57919161--57919204	24	1.9	24	86	9	65	36	6	0	56	1.26
57919159--57919219	32	1.9	32	86	6	88	36	8	0	55	1.30
57919171--57919212	22	1.9	22	90	0	66	35	7	0	57	1.26
57919170--57919219	22	2.3	21	83	10	64	34	8	0	58	1.28
57919388--57919422	16	2.2	16	89	0	52	25	2	2	68	1.17
57921819--57921881	26	2.4	26	81	0	72	50	3	6	39	1.44
57921991--57922033	2	21.5	2	95	0	77	46	0	2	51	1.13
57922365--57922436	27	2.7	28	79	10	71	58	4	8	29	1.46
57927765--57927816	16	3.2	16	97	0	95	25	0	34	40	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57927797--57927887	45	2.0	45	85	2	121	27	6	28	37	1.82
57928034--57928617	121	4.8	121	95	1	1010	48	6	2	43	1.40
57928034--57928617	243	2.4	243	94	1	1021	48	6	2	43	1.40
57928570--57928638	16	4.4	16	71	20	65	42	10	0	47	1.37
57932946--57933001	21	2.6	21	88	2	76	37	25	14	23	1.92
57938042--57938128	31	2.9	29	72	5	75	48	2	1	48	1.21
57938294--57938324	16	1.9	16	93	0	53	45	25	19	9	1.81
57945900--57946517	132	4.7	132	91	1	952	27	19	25	27	1.99
57946990--57947020	16	1.9	16	93	0	53	45	25	19	9	1.81
57948037--57948086	3	16.7	3	100	0	100	32	0	0	68	0.90
57950171--57950230	20	3.0	21	72	16	63	43	3	5	48	1.41
57952738--57952764	2	13.5	2	100	0	54	51	0	0	48	1.00
57953106--57953141	15	2.3	15	95	4	63	52	8	0	38	1.32
57953809--57953848	10	4.2	10	84	15	50	40	0	2	57	1.12
57953809--57953857	18	2.7	18	84	9	55	40	0	4	55	1.19
57953891--57953981	17	5.3	17	75	13	80	46	1	3	49	1.25
57953891--57953984	9	10.9	9	68	16	56	46	1	3	48	1.25
57953891--57953985	25	3.7	26	75	9	88	46	1	3	49	1.24
57953786--57953941	80	2.0	78	81	5	179	42	5	3	48	1.43
57953900--57953985	8	10.1	8	71	12	55	46	0	3	50	1.18
57953968--57954103	59	2.2	61	92	3	222	38	2	3	54	1.33
57954183--57954214	15	2.3	15	89	10	50	75	0	0	25	0.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57954514--57954609	31	3.1	31	93	3	165	44	14	9	31	1.77
57954975--57955045	21	3.5	20	72	16	67	52	0	2	45	1.15
57954986--57955041	9	6.0	9	76	15	51	53	0	3	42	1.18
57955140--57955330	99	1.9	97	89	2	292	30	14	12	42	1.82
57955130--57955359	99	2.4	97	85	4	284	29	16	14	39	1.89
57959159--57959199	4	10.2	4	100	0	82	51	24	0	24	1.49
57965062--57965091	7	4.4	7	95	4	53	26	0	0	73	0.84
57967819--57967852	10	3.6	10	84	15	54	23	0	0	76	0.79
57967819--57967857	18	2.1	19	95	4	71	23	0	2	74	0.94
57968228--57968286	31	1.9	31	89	6	93	35	10	0	54	1.34
57973744--57973810	34	1.9	35	87	3	100	46	13	7	32	1.71
57975326--57975372	24	1.9	24	83	12	60	34	21	0	44	1.52
57977720--57977773	25	2.2	25	96	0	99	46	12	16	24	1.82
57978059--57978093	17	2.0	18	88	5	54	74	2	0	22	0.95
57978057--57978092	19	1.9	19	88	5	56	75	2	0	22	0.94
57985625--57985669	19	2.3	19	84	7	54	60	8	0	31	1.28
57985640--57985677	19	2.0	20	94	5	69	57	5	0	36	1.21
57987854--57988082	116	1.9	119	86	6	333	31	18	10	39	1.85
57994998--57995048	18	2.7	19	84	6	59	37	0	0	62	0.95
58000985--58001029	22	2.0	22	100	0	90	64	4	0	31	1.13
58015225--58015286	32	1.9	32	83	6	81	33	4	4	56	1.42
58018921--58018982	32	1.9	32	83	6	81	33	4	4	56	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
58023792--58023842	21	2.4	21	96	0	93	21	43	11	23	1.85
58024459--58024524	12	5.5	11	83	3	60	36	33	3	27	1.72
58024471--58024524	24	2.2	24	93	0	90	37	33	3	25	1.74
58025301--58025343	16	2.7	16	85	7	61	55	9	32	2	1.44
58026029--58026055	2	13.5	2	100	0	54	51	0	0	48	1.00
58028771--58028828	31	1.9	30	82	10	73	62	13	5	18	1.50
58052850--58052888	21	2.0	20	85	10	53	38	2	0	58	1.12
58055757--58055797	21	2.0	21	85	0	55	53	0	0	46	1.00
58056253--58056281	3	9.7	3	100	0	58	31	0	0	68	0.89
58058702--58058735	11	3.1	11	91	0	50	85	0	14	0	0.60
58059568--58059609	21	2.0	21	100	0	84	19	19	9	52	1.72
58060575--58060641	24	2.8	24	84	4	91	22	23	13	40	1.89
58072553--58072597	21	2.1	22	87	4	65	62	0	0	37	0.96
58076653--58076714	25	2.3	26	83	8	72	59	1	4	33	1.28
58077400--58077434	16	2.2	16	89	0	52	71	14	8	5	1.29
58078269--58078481	44	4.8	44	71	9	164	28	24	18	28	1.98
58078198--58078505	132	2.3	133	90	2	485	29	24	17	28	1.97
58078198--58078549	132	2.6	131	85	4	384	28	25	18	28	1.98
58079791--58079840	23	2.2	23	85	7	66	12	20	0	68	1.21
58080269--58080374	1	106.0	1	71	0	77	2	4	6	85	0.80
58080272--58080374	52	2.0	52	84	3	136	2	4	6	85	0.82
58086915--58086974	25	2.3	26	83	8	70	60	1	5	33	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
58087583--58087617	16	2.2	16	89	0	52	71	14	8	5	1.29
58091807--58091854	21	2.4	21	89	6	73	16	35	22	25	1.95
58092128--58092222	41	2.3	41	90	3	156	15	20	25	38	1.92
58092190--58092464	43	6.4	43	82	2	329	23	20	30	25	1.98
58092210--58092477	129	2.1	130	88	2	396	23	19	30	26	1.98
58092561--58092603	22	2.0	22	90	0	68	44	27	18	9	1.80
58093060--58093254	41	4.8	41	88	1	257	22	20	29	28	1.98
58093060--58093254	81	2.4	82	86	0	257	22	20	29	28	1.98
58093606--58093665	14	4.2	14	81	8	68	23	1	41	33	1.64
58093606--58093647	7	6.0	7	88	0	57	23	0	42	33	1.55
58093613--58093666	7	7.6	7	79	4	54	22	1	44	31	1.63
58093606--58093665	29	2.1	28	84	9	77	23	1	41	33	1.64
58093613--58093673	14	4.4	13	84	10	59	22	1	44	31	1.63
58103534--58103600	31	2.2	31	86	2	91	37	14	38	8	1.78
58113609--58113650	22	1.9	22	90	0	66	40	16	9	33	1.81
58114902--58114935	16	2.1	17	88	5	52	47	0	0	52	1.00
58125042--58125081	19	2.1	19	90	9	64	80	2	7	10	1.00
58133611--58133924	105	3.0	105	82	1	344	34	12	22	31	1.91
58147511--58147544	14	2.5	14	90	4	52	50	32	0	17	1.47
58147956--58148031	22	3.5	22	85	0	107	30	14	26	28	1.95
58151972--58152025	22	2.5	22	82	11	67	42	0	0	57	0.98
58151967--58152025	17	3.7	17	73	17	63	40	0	1	57	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
58154074--58154111	2	19.0	2	100	0	76	50	0	0	50	1.00
58156297--58156425	37	3.5	37	95	0	231	25	18	17	37	1.93
58156389--58156596	52	4.3	46	88	8	254	27	22	14	35	1.93
58156432--58156596	52	3.2	52	94	0	276	27	23	13	35	1.93
58159910--58159965	24	2.3	24	74	17	62	41	21	19	17	1.91
58161591--58161661	31	2.4	29	83	4	88	36	2	7	53	1.43
58161858--58161882	12	2.1	12	100	0	50	32	16	20	32	1.94
58170414--58170462	25	2.0	24	96	4	89	42	0	0	57	0.99
58173229--58173253	2	12.5	2	100	0	50	48	0	0	52	1.00
58177189--58177244	12	4.7	12	73	8	51	19	58	5	16	1.56

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