genome.fa.s2.2.7.7.80.10.50.1000.13.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: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62769430

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   

This is table  13  of  206  ( 24623 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)
3858525--3859121	113	5.4	110	81	5	630	29	19	15	35	1.93
3860929--3860953	12	2.1	12	100	0	50	32	16	36	16	1.90
3882260--3882311	19	2.7	19	80	11	61	46	5	0	48	1.26
3883712--3883742	2	15.5	2	100	0	62	51	0	0	48	1.00
3886044--3886108	31	2.1	31	85	0	85	36	6	10	46	1.64
3889317--3889382	29	2.3	29	81	2	71	24	16	18	40	1.90
3898101--3898181	37	2.2	37	95	0	144	24	11	20	43	1.85
3901021--3901051	6	5.2	6	100	0	62	16	0	0	83	0.64
3907737--3907800	23	2.9	21	78	19	67	23	6	0	70	1.10
3907732--3907781	25	1.9	26	88	8	75	20	6	0	74	1.03
3907758--3907791	12	2.8	12	87	12	52	23	5	0	70	1.09
3907731--3907784	16	3.5	15	80	12	56	20	5	0	74	1.02
3911530--3911560	14	2.2	14	100	0	62	29	6	35	29	1.82
3920969--3921513	273	2.0	273	85	2	729	31	17	19	31	1.95
3923529--3923576	17	2.8	17	81	15	62	47	0	6	45	1.27
3924549--3924575	14	1.9	14	100	0	54	51	3	0	44	1.19
3928382--3928440	31	1.9	31	89	3	93	33	3	1	61	1.23
3928881--3928910	15	1.9	16	93	6	53	76	6	3	13	1.11
3929408--3929432	11	2.3	11	100	0	50	28	0	8	64	1.22
3942126--3942158	2	16.5	2	93	0	57	45	0	0	54	0.99
3944609--3944638	5	5.8	5	92	7	51	43	0	0	56	0.99
3972845--3972877	3	11.0	3	100	0	66	0	33	0	66	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4007909--4007974	30	2.2	31	83	2	80	39	1	7	51	1.40
4011242--4011298	30	1.9	30	88	0	87	29	19	5	45	1.72
4016457--4016491	12	3.0	12	87	4	54	65	0	0	34	0.93
4016866--4016926	32	1.9	32	86	6	88	31	19	13	36	1.90
4021354--4021450	43	2.3	42	87	8	151	30	25	15	27	1.96
4022154--4022180	5	5.4	5	100	0	54	81	0	0	18	0.69
4024532--4024569	13	2.8	14	88	8	60	36	5	0	57	1.21
4025174--4025202	8	3.8	8	90	9	51	37	37	0	24	1.56
4025237--4025316	21	3.8	21	69	12	58	41	32	0	26	1.56
4025940--4026340	41	9.8	40	85	3	451	28	29	19	21	1.98
4031316--4031348	16	2.1	16	100	0	66	18	12	33	36	1.88
4035154--4035214	34	1.9	33	83	12	83	22	18	16	42	1.89
4036708--4036732	11	2.3	11	100	0	50	40	8	0	52	1.31
4036747--4036833	22	4.1	22	70	24	71	34	2	0	63	1.07
4036708--4036845	51	2.7	52	87	5	201	34	2	0	62	1.10
4046662--4046692	16	2.0	16	93	6	55	0	12	6	80	0.89
4053596--4053668	38	1.9	38	94	0	128	42	8	21	27	1.81
4054065--4054096	16	1.9	17	93	6	57	56	0	0	43	0.99
4061512--4061570	30	2.0	30	83	6	75	49	0	0	50	1.00
4072934--4073068	41	3.3	41	91	0	225	26	28	16	28	1.97
4073238--4073334	41	2.4	41	91	0	158	26	27	17	27	1.98
4073558--4073599	2	21.5	2	90	4	68	52	0	0	47	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4076772--4076916	50	2.9	50	84	1	191	21	29	22	26	1.99
4077260--4077316	30	1.9	30	89	3	89	31	24	3	40	1.72
4080551--4080586	16	2.2	16	95	0	63	22	25	19	33	1.97
4086717--4086767	23	2.2	23	96	0	93	45	7	7	39	1.62
4087048--4087099	2	26.0	2	92	0	86	50	3	0	46	1.20
4088456--4088514	22	2.8	19	78	19	55	55	0	3	40	1.16
4096859--4096907	17	3.1	16	76	18	50	16	12	28	42	1.84
4097258--4097808	131	4.2	130	81	5	587	24	23	21	30	1.99
4097389--4097876	175	2.8	175	95	1	879	24	24	21	30	1.99
4097262--4097811	44	12.7	44	78	5	499	24	23	21	30	1.99
4097352--4097876	131	4.0	129	78	7	449	24	24	21	30	1.99
4097889--4098351	87	5.2	87	87	5	656	22	22	25	29	1.99
4097956--4098324	88	4.0	94	85	10	505	21	23	25	29	1.99
4097958--4098324	185	2.0	184	92	1	619	21	23	25	29	1.99
4099574--4099624	7	7.0	7	76	24	52	15	15	0	68	1.21
4104495--4104523	12	2.3	13	94	5	51	75	0	0	24	0.80
4104577--4104610	2	17.0	2	100	0	68	50	0	0	50	1.00
4104774--4104869	3	31.0	3	79	14	97	62	2	3	32	1.22
4114365--4114433	29	2.3	29	85	5	84	49	11	14	24	1.77
4118013--4118051	20	2.0	20	94	0	69	48	2	0	48	1.15
4121284--4121325	21	2.0	21	95	0	75	45	4	30	19	1.71
4136514--4136561	16	2.9	17	75	12	55	64	4	0	31	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4136704--4136759	29	1.9	29	82	7	69	62	5	1	30	1.28
4136935--4136999	28	2.2	30	84	13	82	26	3	0	70	1.01
4136947--4137001	26	2.0	28	86	10	78	30	1	0	67	1.01
4140552--4140598	23	2.1	23	88	4	69	14	4	6	74	1.17
4147530--4147595	34	1.9	34	100	0	132	43	9	21	25	1.81
4171485--4171523	18	2.1	19	85	4	53	56	2	0	41	1.13
4171544--4171591	22	2.2	22	81	7	53	54	2	6	37	1.38
4173096--4173196	38	2.6	39	85	4	132	32	8	0	57	1.36
4173138--4173200	19	3.3	19	71	22	51	30	6	1	61	1.30
4176132--4176158	2	13.5	2	100	0	54	48	0	0	51	1.00
4179071--4179100	14	2.1	14	93	0	51	80	10	0	10	0.92
4193094--4193123	16	1.9	16	93	6	53	73	0	0	26	0.84
4195168--4195259	41	2.2	41	83	9	114	35	23	17	22	1.95
4196185--4196228	2	24.0	2	82	17	60	52	0	0	47	1.00
4196185--4196228	9	4.8	10	81	18	60	52	0	0	47	1.00
4196187--4196228	17	2.4	17	88	8	57	52	0	0	47	1.00
4196188--4196230	5	8.4	5	87	7	52	53	0	0	46	1.00
4196184--4196273	23	4.0	23	71	17	73	52	2	0	45	1.13
4197783--4197876	13	7.2	13	78	16	97	76	1	3	19	0.98
4197793--4197882	5	18.2	5	74	21	75	78	1	1	18	0.87
4197795--4197882	18	4.8	17	79	19	97	79	1	1	18	0.86
4197795--4197877	16	5.1	15	77	16	69	79	1	1	18	0.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4204207--4204243	10	3.7	10	96	0	65	62	0	10	27	1.28
4206298--4206361	31	2.1	31	91	2	103	29	1	9	59	1.38
4206485--4206517	11	2.9	12	86	13	52	66	0	0	33	0.92
4214911--4215031	63	1.9	63	89	0	188	23	23	29	23	1.99
4226826--4226850	7	3.6	7	100	0	50	28	0	12	60	1.32
4227940--4228062	25	5.1	25	76	13	141	42	0	14	43	1.45
4228065--4228101	9	4.2	9	96	3	67	29	0	10	59	1.31
4228116--4228376	120	2.2	120	92	1	434	52	20	3	23	1.63
4228137--4228392	23	10.9	23	85	4	332	51	21	3	23	1.63
4229649--4229988	124	2.7	124	90	2	538	32	20	17	29	1.96
4233442--4233513	28	2.5	29	74	19	71	34	5	5	54	1.47
4242599--4242632	17	1.9	18	88	5	52	29	8	2	58	1.43
4242598--4242664	18	3.6	18	76	9	55	37	5	1	55	1.34
4242617--4242671	9	5.8	9	77	12	56	40	3	0	56	1.17
4242619--4242671	20	2.8	20	81	13	58	39	3	0	56	1.17
4242628--4242676	20	2.4	21	83	12	59	40	4	0	55	1.19
4242827--4242908	9	8.8	9	75	11	60	30	1	6	62	1.27
4246784--4246833	26	2.0	25	84	4	64	28	2	6	64	1.28
4246878--4246930	20	2.5	22	78	9	65	41	3	1	52	1.30
4250558--4250674	39	3.0	40	89	2	182	39	2	0	57	1.18
4250591--4250663	17	4.0	17	73	22	58	39	1	1	57	1.16
4250568--4250673	11	10.4	11	67	25	63	40	2	0	55	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4250694--4250718	5	5.0	5	100	0	50	0	40	60	0	0.97
4254854--4254891	19	2.1	19	85	14	53	18	5	0	76	0.97
4258106--4258161	24	2.4	23	77	11	60	64	1	0	33	1.04
4268471--4268517	23	2.1	23	84	4	60	48	0	2	48	1.13
4271883--4271911	10	2.9	10	100	0	58	17	10	0	72	1.11
4275008--4275171	87	1.9	86	89	3	258	40	21	7	29	1.81
4275267--4275297	8	3.9	8	100	0	62	51	0	0	48	1.00
4275311--4275370	18	3.2	18	76	4	66	70	1	1	26	1.07
4275318--4275371	28	1.9	28	85	7	74	64	1	1	31	1.14
4275487--4275546	17	3.5	16	76	19	59	73	0	3	23	0.98

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