genome.fa.s1.2.7.7.80.10.50.1000.164.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  164  of  187  ( 22383 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)
48299705--48299815	50	2.2	51	93	1	188	33	14	24	27	1.94
48310110--48310272	44	3.6	44	81	11	202	31	14	23	30	1.94
48310164--48310274	50	2.2	51	91	1	179	34	14	23	27	1.94
48320691--48320760	33	2.1	33	100	0	140	30	8	30	31	1.87
48324821--48324902	31	3.0	25	70	24	67	43	15	0	40	1.47
48330681--48330752	24	3.0	24	100	0	144	37	16	12	33	1.86
48336488--48336527	21	1.9	21	84	0	53	52	0	0	47	1.00
48348950--48348976	2	13.5	2	100	0	54	48	0	0	51	1.00
48356818--48356873	25	2.2	25	81	12	62	42	5	3	48	1.43
48362496--48362553	27	2.2	26	84	3	71	37	20	5	36	1.75
48366358--48366417	30	2.0	30	96	0	111	40	26	5	28	1.77
48366985--48367044	30	2.0	31	86	3	86	40	0	40	20	1.52
48367258--48367294	9	4.1	9	85	0	56	27	10	16	45	1.80
48368721--48368758	17	2.3	17	86	13	53	63	26	0	10	1.27
48368721--48368766	17	2.8	17	83	9	51	65	21	0	13	1.26
48375295--48375334	14	2.9	14	84	0	53	32	7	17	42	1.77
48375456--48375493	20	1.9	19	94	5	67	50	2	0	47	1.15
48378184--48378233	25	2.0	25	88	0	73	60	2	32	6	1.32
48379172--48379249	38	2.0	39	85	11	108	30	5	3	60	1.36
48379172--48379229	19	3.1	19	82	9	73	31	5	5	58	1.42
48384136--48384211	27	2.8	27	95	0	134	31	19	27	21	1.97
48384112--48384231	52	2.3	52	77	11	129	32	20	28	18	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48391013--48391102	30	3.0	29	83	4	117	33	17	13	35	1.89
48393482--48393577	51	1.9	49	82	4	120	31	18	7	42	1.78
48396101--48396132	6	5.3	6	100	0	64	31	0	50	18	1.48
48398394--48398420	13	2.1	13	100	0	54	29	48	0	22	1.51
48420794--48420844	21	2.4	21	78	12	52	62	5	0	31	1.19
48421968--48422160	44	4.6	42	80	9	216	41	12	7	38	1.71
48421968--48422127	37	4.0	38	77	12	151	40	12	7	39	1.71
48422682--48422865	92	2.0	92	98	0	359	47	6	8	37	1.60
48440570--48440642	27	2.7	25	75	14	65	27	5	1	65	1.22
48440814--48441040	43	5.3	43	87	0	294	21	18	31	29	1.96
48440809--48441040	129	1.8	127	87	3	349	21	17	31	29	1.96
48441134--48441176	22	2.0	22	95	0	77	41	27	20	9	1.83
48444072--48444290	32	6.7	32	83	4	258	33	10	14	42	1.79
48444072--48444290	64	3.4	64	87	3	312	33	10	14	42	1.79
48446307--48446493	41	4.6	41	87	2	268	29	17	26	27	1.97
48446498--48446613	43	2.8	41	81	6	133	21	17	25	35	1.95
48469126--48469316	93	2.1	93	93	2	330	41	17	13	26	1.87
48472453--48472506	21	2.6	21	84	0	63	38	7	25	27	1.83
48482107--48482168	27	2.3	27	86	5	81	24	24	9	41	1.84
48486627--48486669	21	2.2	19	87	8	59	58	4	2	34	1.32
48486627--48486668	20	2.2	19	87	12	59	57	4	2	35	1.33
48494377--48494577	43	4.7	43	85	2	278	37	22	16	22	1.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48501981--48502030	25	2.0	25	88	7	75	42	10	10	38	1.72
48503415--48503450	15	2.4	15	90	0	54	0	25	0	75	0.81
48503408--48503457	24	2.1	23	85	3	64	0	24	0	76	0.80
48503409--48503457	23	2.1	23	85	7	64	0	24	0	75	0.80
48505566--48505620	29	1.9	28	85	3	74	21	5	12	60	1.53
48506485--48506523	19	2.1	19	85	0	51	51	10	0	38	1.36
48523305--48523345	20	2.0	20	90	0	64	17	26	2	53	1.56
48523608--48523799	50	3.8	50	83	0	231	23	27	19	28	1.99
48524136--48524194	30	2.0	30	86	0	82	32	23	5	38	1.77
48528299--48528364	22	3.0	22	77	2	78	22	18	27	31	1.97
48528412--48528495	28	3.0	28	78	0	96	27	15	23	33	1.95
48530842--48530906	32	2.1	32	97	2	123	30	9	12	47	1.72
48531526--48531556	12	2.6	12	100	0	62	74	19	6	0	1.03
48537313--48537377	32	2.1	32	97	2	123	30	9	12	47	1.72
48538285--48538325	19	2.2	19	86	0	55	46	12	4	36	1.63
48545524--48545558	19	1.9	18	88	11	54	28	2	5	62	1.32
48546339--48546374	17	2.1	18	89	5	56	55	0	5	38	1.23
48547053--48547098	14	3.4	14	78	3	58	65	0	0	34	0.93
48547057--48547117	29	2.1	30	82	11	74	60	0	1	37	1.07
48548155--48548210	9	5.5	11	72	25	52	0	21	0	78	0.75
48548155--48548215	20	3.2	18	82	15	70	0	19	0	80	0.72
48548155--48548216	18	3.4	17	75	16	61	0	20	0	79	0.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48548155--48548220	19	3.4	19	78	14	73	0	22	0	77	0.77
48548442--48548488	9	5.3	9	85	10	53	2	21	0	76	0.89
48548453--48548505	19	2.8	19	85	2	63	0	28	0	71	0.86
48548867--48548996	59	2.2	59	83	8	167	43	4	16	34	1.69
48548867--48548996	29	4.4	29	84	4	163	43	4	16	34	1.69
48549396--48551316	78	24.9	77	80	9	2007	35	20	16	27	1.94
48549140--48551310	230	9.3	229	86	6	2945	35	20	16	27	1.94
48549140--48551318	78	28.0	79	75	12	1490	35	20	16	27	1.94
48551887--48551944	20	3.0	20	80	12	66	3	1	8	86	0.76
48551887--48551945	19	3.1	19	83	9	75	5	1	8	84	0.82
48551888--48551944	11	5.2	11	81	8	62	1	1	8	87	0.68
48551888--48551936	1	49.0	1	79	0	53	2	2	6	89	0.62
48557910--48558004	40	2.4	40	89	0	154	32	22	15	29	1.95
48562951--48563012	21	3.1	20	84	13	83	0	20	0	79	0.74
48562951--48563012	9	6.3	9	78	15	61	0	20	0	79	0.74
48563157--48563191	15	2.3	15	100	0	70	0	11	11	77	1.00
48563288--48563325	8	4.8	8	83	9	51	0	13	0	86	0.56
48563295--48563329	8	3.9	9	88	11	54	0	14	0	85	0.59
48563292--48563356	3	21.3	3	80	9	60	0	24	0	75	0.81
48563288--48563356	9	7.7	9	85	10	70	0	23	0	76	0.78
48563420--48563468	20	2.6	19	84	9	57	2	30	0	67	1.02
48563719--48563884	59	2.8	58	85	4	188	46	3	16	33	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48563719--48563884	29	5.6	29	81	7	174	46	3	16	33	1.64
48566762--48567378	83	7.5	83	78	10	503	42	12	14	30	1.82
48567165--48567319	74	2.1	74	92	0	256	42	10	14	31	1.81
48567078--48567379	160	1.9	161	87	0	444	42	12	13	31	1.82
48567505--48567548	22	2.0	23	86	4	63	65	2	0	31	1.05
48567507--48567577	30	2.4	31	81	11	87	59	1	1	38	1.15
48567978--48568018	20	2.0	20	85	0	55	51	4	9	34	1.56
48569587--48569623	16	2.2	17	90	4	58	45	0	2	51	1.15
48571217--48571277	23	2.5	26	79	15	76	31	22	24	21	1.98
48576251--48576313	21	3.2	21	66	25	64	33	3	14	49	1.59
48576251--48576328	38	2.1	38	100	0	156	33	2	15	48	1.58
48576338--48576407	29	2.3	29	87	4	95	24	14	14	47	1.81
48577586--48577619	14	2.5	14	95	4	61	50	35	0	14	1.44
48578340--48578398	22	2.7	22	79	7	59	50	3	1	44	1.28
48578365--48578536	11	16.9	11	73	19	133	58	0	1	40	1.06
48578366--48578497	10	13.3	9	75	16	77	56	0	0	43	1.04
48578389--48578555	39	4.3	39	90	3	273	60	0	0	38	1.01
48578366--48578536	50	3.4	50	81	10	163	58	0	1	40	1.06
48578520--48578564	16	2.7	17	79	6	56	60	0	0	40	0.97
48581669--48581702	7	4.9	7	86	13	52	29	0	0	70	0.87
48591768--48591830	32	2.0	32	87	0	90	17	30	9	42	1.81
48594234--48594347	43	2.7	42	83	2	122	36	24	17	21	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48601585--48601782	108	1.8	108	89	2	308	38	16	21	23	1.93
48611308--48611382	31	2.5	31	88	2	107	44	12	21	22	1.85
48611371--48611527	29	5.3	29	79	9	174	42	10	26	19	1.84
48611373--48611527	59	2.6	58	77	13	181	42	10	27	19	1.84
48611331--48611543	89	2.4	89	84	2	284	42	12	23	22	1.87
48611519--48611588	30	2.3	30	82	0	95	34	14	30	21	1.93
48613196--48613324	69	1.9	67	87	6	188	41	3	3	51	1.36
48615802--48615841	21	1.9	21	100	0	80	70	10	10	10	1.36
48619745--48619777	12	2.8	12	100	0	66	30	15	0	54	1.41
48624642--48624715	38	1.9	38	86	5	105	27	8	2	62	1.37

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