genome.fa.s4.2.7.7.80.10.50.1000.13.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: 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  13  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)
4179790--4179886	31	3.2	31	84	10	94	62	0	2	35	1.07
4179806--4179848	11	3.8	11	78	6	50	60	0	2	37	1.10
4179791--4179878	41	2.1	42	91	8	144	61	0	2	36	1.09
4179831--4179905	27	2.7	28	88	11	118	60	0	2	37	1.11
4179809--4179933	38	3.2	38	82	10	139	63	0	3	33	1.11
4179887--4179916	11	2.6	12	89	10	53	50	0	6	43	1.28
4179790--4179934	68	2.1	70	88	6	215	62	0	2	34	1.09
4180844--4180877	2	17.0	2	93	0	59	52	0	0	47	1.00
4182080--4182136	24	2.4	24	96	0	105	24	31	10	33	1.89
4187828--4187918	39	2.3	40	83	7	114	43	9	3	42	1.54
4188793--4188831	20	2.0	20	89	0	60	30	10	10	48	1.70
4196232--4196401	39	4.5	39	87	10	214	39	2	0	58	1.11
4196263--4196338	8	8.2	9	71	23	52	39	1	0	59	1.06
4197531--4197574	20	2.2	20	91	0	70	43	15	6	34	1.74
4197653--4197705	16	3.2	16	94	5	97	24	0	37	37	1.56
4197941--4197975	18	2.0	17	88	5	52	54	0	0	45	0.99
4200355--4200389	18	1.9	18	100	0	70	60	0	28	11	1.32
4203612--4203650	13	3.1	13	81	7	53	41	0	0	58	0.98
4204118--4204172	2	27.5	2	100	0	110	49	0	0	50	1.00
4214603--4214630	7	4.0	7	100	0	56	57	0	14	28	1.38
4215208--4215241	16	2.1	17	88	5	52	58	2	0	38	1.13
4216093--4216165	20	3.7	19	68	15	58	35	4	1	58	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4227838--4227886	19	2.6	19	87	12	66	14	14	10	61	1.57
4227818--4227886	20	3.5	20	78	11	79	15	14	11	57	1.64
4229307--4229432	43	2.9	43	78	9	123	32	19	23	23	1.98
4229452--4229533	44	1.9	42	82	9	103	43	18	15	21	1.87
4230566--4230607	15	2.9	15	79	17	52	42	4	0	52	1.22
4230550--4230607	29	2.0	29	82	0	71	41	5	3	50	1.42
4230570--4230607	14	2.6	15	84	16	53	44	5	0	50	1.24
4231226--4231318	20	4.6	21	74	12	79	21	19	6	52	1.68
4231226--4231325	21	5.0	21	73	14	79	21	19	8	52	1.71
4231504--4231549	19	2.3	20	88	3	67	10	15	4	69	1.32
4240826--4240857	4	8.0	4	100	0	64	25	0	0	75	0.81
4247994--4248027	14	2.4	14	90	0	50	35	17	2	44	1.64
4248539--4248575	20	1.9	19	89	10	58	48	0	2	48	1.15
4251747--4252367	44	14.1	44	65	8	134	30	23	17	28	1.97
4251659--4252571	132	6.9	132	89	1	1278	30	23	17	28	1.97
4253898--4254072	1	175.0	1	70	0	107	0	1	13	84	0.70
4253898--4254071	6	28.8	6	95	3	289	0	1	13	84	0.70
4258084--4258280	98	2.0	98	94	0	349	37	24	10	27	1.88
4259614--4259726	19	5.8	19	91	4	190	37	15	9	38	1.80
4259614--4259725	40	2.8	40	97	2	210	37	14	9	38	1.79
4259607--4259726	59	2.1	56	90	6	188	37	15	9	38	1.79
4262295--4262402	25	4.3	25	80	4	74	17	24	21	37	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4262320--4262450	50	2.6	50	83	7	142	21	23	22	32	1.98
4262345--4262450	25	4.2	25	76	7	99	22	23	22	31	1.99
4262295--4262450	75	2.1	75	79	4	163	20	23	20	35	1.96
4262318--4262469	50	3.0	50	80	7	123	23	23	19	33	1.97
4284805--4284842	13	2.9	13	84	0	58	42	18	5	34	1.73
4295733--4295799	34	1.9	35	84	3	91	32	10	11	44	1.75
4295789--4295865	33	2.4	32	82	4	91	27	9	16	46	1.77
4297142--4297211	27	2.6	27	80	8	79	51	20	2	25	1.61
4300873--4300904	16	2.0	16	100	0	64	56	6	31	6	1.49
4304429--4304527	41	2.4	42	84	5	130	21	20	21	37	1.95
4304844--4304913	21	3.3	21	89	0	104	2	44	20	32	1.66
4309429--4309610	9	20.9	9	76	8	162	31	2	20	45	1.63
4309422--4309610	34	5.4	35	76	9	149	31	2	20	46	1.62
4309590--4309671	37	2.2	37	89	2	121	37	4	9	47	1.58
4309659--4309697	20	2.0	20	94	0	69	46	5	5	43	1.48
4309589--4309763	94	1.9	93	89	1	269	37	5	9	48	1.59
4309679--4309853	37	4.7	37	95	0	305	34	5	10	49	1.60
4309850--4309946	37	2.6	37	95	0	176	36	5	9	49	1.57
4309757--4309996	93	2.6	93	96	0	435	36	4	9	49	1.56
4309887--4309996	56	2.0	56	92	0	184	38	3	9	49	1.52
4312086--4312428	147	2.3	146	81	2	384	37	21	13	27	1.91
4312529--4312565	19	1.9	19	94	0	65	29	29	13	27	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4313748--4314131	114	3.4	111	78	8	391	27	27	21	23	1.99
4314164--4314254	40	2.3	40	96	0	173	17	27	23	31	1.97
4314164--4314270	40	2.7	40	89	2	144	17	26	25	30	1.97
4314382--4314406	2	12.5	2	100	0	50	52	0	0	48	1.00
4314597--4314730	59	2.2	61	80	10	152	35	17	6	40	1.76
4315224--4315354	57	2.3	55	80	8	131	40	12	11	35	1.79
4315552--4315586	18	1.9	18	94	0	61	54	2	0	42	1.15
4318266--4318321	30	2.0	27	83	13	69	42	0	0	57	0.99
4320174--4320223	25	2.0	25	84	7	66	50	0	8	42	1.32
4321982--4322016	17	1.9	19	88	11	56	65	11	2	20	1.37
4328253--4328296	21	2.1	21	86	0	61	40	11	13	34	1.81
4329300--4329342	23	2.0	21	86	13	61	65	2	0	32	1.06
4329407--4329455	11	4.5	11	76	0	53	67	6	2	24	1.24
4329413--4329458	22	2.2	22	84	7	60	69	4	2	23	1.17
4333679--4334076	45	8.8	45	85	1	510	30	13	22	33	1.93
4335604--4335649	3	15.0	3	86	4	65	36	0	0	63	0.95
4335595--4335646	25	2.1	25	85	0	68	34	3	0	61	1.14
4338922--4338953	16	2.0	16	93	0	55	43	15	6	34	1.72
4346242--4346273	11	3.1	11	91	8	50	65	6	0	28	1.16
4348249--4348273	2	12.5	2	100	0	50	0	48	0	52	1.00
4349906--4350043	44	3.1	44	96	0	258	38	13	5	42	1.68
4350622--4350698	13	5.9	13	89	0	118	40	24	9	25	1.85
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4353496--4353530	16	2.3	15	95	5	61	37	8	20	34	1.83
4366518--4366578	21	2.9	21	83	11	72	47	4	6	40	1.51
4366514--4366565	21	2.6	21	88	11	74	46	3	5	44	1.45
4375215--4375279	14	4.7	14	74	16	55	49	6	4	40	1.48
4377161--4377203	23	1.9	22	86	13	61	67	11	0	20	1.22
4378316--4378620	43	7.2	42	71	12	207	28	22	21	27	1.99
4378316--4378707	126	3.1	126	92	1	615	28	21	20	28	1.98
4378712--4379007	50	5.9	49	75	6	200	26	24	20	28	1.99
4378713--4378971	100	2.6	100	87	3	362	25	25	20	27	1.99
4378797--4379069	150	1.8	149	87	0	402	24	23	21	29	1.99
4378797--4379021	50	4.5	50	79	2	254	25	23	20	30	1.99
4379157--4379340	100	1.8	100	83	2	244	26	24	21	28	1.99
4379368--4379544	88	2.0	88	88	2	266	24	25	22	27	2.00
4380774--4380811	13	2.8	13	88	4	58	10	15	2	71	1.25
4386176--4386218	23	1.9	22	86	13	61	67	11	0	20	1.22
4386639--4386686	20	2.4	20	86	6	62	66	2	6	25	1.26
4386694--4386776	21	4.3	18	66	22	53	59	1	8	31	1.35
4386799--4386828	15	2.0	15	93	0	51	56	0	0	43	0.99
4391763--4391944	41	4.4	41	90	0	283	36	23	15	24	1.93
4393946--4393977	2	16.0	2	100	0	64	50	0	0	50	1.00
4403949--4404001	15	3.5	15	74	5	52	16	9	18	54	1.69
4404246--4404288	5	8.6	5	85	10	61	34	0	0	65	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
4405649--4405702	23	2.3	23	87	0	81	22	40	3	33	1.71
4411330--4411490	43	3.7	43	87	0	196	27	27	18	26	1.98
4411689--4411726	19	2.0	19	94	0	67	57	2	10	28	1.45
4417327--4417352	10	2.6	10	100	0	52	38	19	0	42	1.51
4419527--4419594	15	4.9	14	71	16	52	41	35	0	23	1.55
4419530--4419567	15	2.5	15	86	0	58	36	42	0	21	1.53
4420081--4420270	41	4.6	41	78	6	170	35	23	24	16	1.94
4420121--4420295	41	4.3	41	86	0	197	36	23	24	15	1.93
4420122--4420295	82	2.1	82	84	0	222	36	22	24	15	1.93
4420222--4420359	41	3.4	41	80	4	136	35	23	21	19	1.96

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