genome.fa.s5.2.7.7.80.10.50.1000.178.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: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  64140413

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   207   208   

This is table  178  of  208  ( 24913 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)
54397463--54397502	3	13.3	3	84	10	55	37	0	62	0	0.95
54398397--54398434	2	19.5	2	83	5	51	50	5	0	44	1.24
54399296--54399351	22	2.5	24	80	16	66	33	0	1	64	1.04
54402001--54402075	36	2.1	36	87	4	109	36	26	9	28	1.87
54405895--54405938	18	2.4	18	81	7	54	40	2	2	54	1.25
54405929--54405970	23	1.9	22	85	9	59	33	0	4	61	1.17
54407104--54407166	27	2.3	28	94	2	110	20	14	9	55	1.67
54420182--54420262	19	4.2	18	72	20	65	55	3	1	39	1.25
54420493--54420556	23	2.7	23	76	11	67	31	0	1	67	1.00
54422597--54422688	42	2.2	42	80	0	112	20	39	18	21	1.93
54422597--54422700	42	2.5	41	75	6	109	19	38	18	24	1.93
54424694--54424738	23	1.9	24	81	4	56	33	24	0	42	1.55
54424885--54424937	3	17.7	3	100	0	106	66	0	0	33	0.92
54425451--54425518	32	2.1	32	100	0	136	44	11	17	26	1.83
54425541--54425574	17	2.0	17	88	11	52	0	23	0	76	0.79
54429261--54429393	37	3.6	37	86	3	178	35	30	16	18	1.93
54439849--54439888	19	2.1	19	86	9	55	32	2	5	60	1.32
54445951--54446032	40	2.0	40	100	0	164	40	7	13	39	1.72
54456365--54456402	19	2.0	20	94	5	69	47	5	18	28	1.70
54456612--54456718	19	5.6	19	87	0	160	38	9	13	39	1.76
54456615--54456718	38	2.7	38	96	0	190	39	8	12	39	1.74
54456624--54456744	19	6.0	21	83	4	105	38	7	14	39	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54468537--54468600	29	2.2	29	78	10	78	42	1	1	54	1.19
54478464--54478488	10	2.5	10	100	0	50	40	0	0	60	0.97
54479788--54479837	2	25.0	2	100	0	100	50	0	0	50	1.00
54480381--54480424	2	22.0	2	100	0	88	50	0	0	50	1.00
54483452--54483483	16	2.0	16	93	0	55	59	0	3	37	1.13
54483411--54483482	26	2.8	26	72	8	67	52	0	1	45	1.09
54483497--54483525	5	5.8	5	100	0	58	41	0	0	58	0.98
54486963--54487083	62	2.0	60	80	9	138	38	5	14	42	1.69
54498452--54498521	35	2.0	36	85	2	97	31	12	17	38	1.87
54498017--54498620	301	2.0	304	95	1	1099	37	10	12	39	1.77
54498736--54498765	15	1.9	16	93	6	53	60	0	26	13	1.34
54504254--54504293	20	2.0	20	90	9	64	45	2	2	50	1.28
54505647--54505692	22	2.1	22	100	0	92	28	30	8	32	1.87
54508949--54509011	30	2.1	30	96	0	117	57	15	3	23	1.53
54510752--54510798	16	2.9	16	81	15	60	44	0	0	55	0.99
54526884--54526959	29	2.6	29	87	4	98	47	13	13	26	1.79
54526908--54526981	29	2.5	29	86	8	96	48	14	13	22	1.79
54528409--54528440	12	2.7	12	95	0	55	12	21	21	43	1.86
54538601--54538739	73	1.9	73	96	0	260	45	7	10	36	1.67
54540768--54540860	41	2.3	41	88	0	141	37	18	19	24	1.94
54540824--54540893	33	2.1	33	94	0	122	32	22	22	21	1.98
54545458--54545497	18	2.2	18	86	0	53	40	45	2	12	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54545608--54545648	18	2.3	18	91	0	64	26	4	19	48	1.69
54545721--54545745	12	2.1	12	100	0	50	16	24	36	24	1.94
54546895--54546920	13	2.0	13	100	0	52	23	30	15	30	1.95
54549276--54549330	21	2.6	21	91	0	92	21	9	38	30	1.85
54556961--54557008	8	5.9	8	78	4	51	6	6	4	83	0.91
54558304--54558336	16	2.1	16	88	5	50	63	12	0	24	1.28
54570165--54570226	29	2.1	29	90	0	97	30	29	12	27	1.93
54577367--54577409	20	2.0	21	82	13	52	46	30	4	18	1.69
54578932--54578964	13	2.6	13	90	4	50	30	6	9	54	1.56
54581492--54581524	13	2.6	13	90	4	50	30	6	9	54	1.56
54600014--54600520	111	4.7	103	73	11	388	32	19	16	31	1.94
54600014--54600579	223	2.6	216	82	5	561	33	18	16	31	1.93
54600306--54600928	104	5.8	104	75	8	333	37	17	16	28	1.91
54600482--54600947	104	4.4	105	77	4	375	38	17	17	26	1.92
54600789--54601106	153	2.0	156	86	4	437	37	18	18	24	1.94
54600897--54600992	45	2.1	45	100	0	192	37	20	22	18	1.94
54601172--54601386	112	1.9	112	81	3	263	40	16	15	27	1.88
54601380--54601487	48	2.2	48	85	6	139	45	15	15	23	1.85
54601750--54601789	5	8.2	5	86	5	55	20	2	2	75	1.04
54606719--54607148	74	5.6	74	85	7	490	25	16	20	36	1.94
54606722--54607148	157	2.8	153	85	6	530	25	16	21	36	1.94
54607341--54607381	5	8.2	5	84	10	57	19	2	0	78	0.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54607342--54607372	14	2.2	14	94	0	53	19	3	0	77	0.90
54608545--54608578	12	2.8	12	86	13	52	82	0	17	0	0.67
54608552--54608587	18	2.0	18	89	10	56	83	2	13	0	0.76
54609162--54609310	18	8.3	18	75	8	124	30	13	10	46	1.76
54609162--54609292	18	7.3	18	76	13	126	30	14	9	45	1.78
54609118--54609302	37	4.9	38	74	15	145	31	12	9	45	1.75
54609152--54609354	90	2.2	90	77	7	214	30	13	9	47	1.74
54609144--54609396	18	13.9	18	72	8	115	31	13	9	46	1.74
54610023--54610303	107	2.6	106	80	7	314	39	15	17	27	1.90
54610058--54610335	107	2.6	107	82	7	355	41	15	16	25	1.88
54610058--54611196	110	10.6	106	71	14	385	35	17	17	29	1.92
54610512--54610683	88	1.9	89	82	7	213	30	15	19	34	1.93
54610655--54611196	110	5.0	109	84	5	684	34	18	18	28	1.94
54610655--54611196	216	2.5	215	84	5	723	34	18	18	28	1.94
54613067--54613096	13	2.3	13	100	0	60	40	43	0	16	1.48
54613242--54613300	9	6.4	9	77	11	66	23	10	25	40	1.86
54613248--54613309	18	3.4	18	79	2	61	24	8	25	41	1.82
54615760--54615806	20	2.3	20	75	13	51	14	8	2	74	1.15
54615863--54615898	12	2.8	13	91	8	65	38	0	16	44	1.48
54615905--54615951	22	2.1	23	92	4	78	51	0	0	48	1.00
54616320--54616367	13	3.5	13	78	15	51	58	0	2	39	1.10
54616432--54616499	7	9.7	7	90	0	109	60	0	0	39	0.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54616881--54616965	40	2.1	41	89	6	129	35	8	4	51	1.53
54616889--54616976	40	2.2	40	82	8	99	36	7	4	51	1.52
54619387--54619453	30	2.2	30	86	0	89	32	25	16	25	1.96
54619398--54619478	30	2.7	30	86	0	99	30	24	16	28	1.96
54622809--54622847	13	3.0	13	85	7	53	46	0	2	51	1.14
54622856--54622915	19	3.0	21	72	18	56	56	0	1	41	1.09
54622947--54622991	21	2.1	22	91	4	74	55	2	0	42	1.12
54622971--54623046	14	5.5	14	68	14	59	55	0	1	43	1.08
54622928--54623089	76	2.1	79	86	7	226	55	1	2	40	1.21
54622893--54623123	112	2.1	110	87	7	324	56	1	1	40	1.18
54623059--54623103	19	2.2	21	88	11	67	60	0	2	37	1.09
54622969--54623127	13	13.1	12	65	26	61	57	0	1	40	1.14
54623207--54623268	19	3.3	18	76	14	54	70	3	6	19	1.22
54623214--54623282	20	3.6	18	77	14	66	75	1	7	15	1.09
54624405--54624488	43	2.0	42	88	6	125	10	8	5	75	1.20
54624482--54624556	23	3.6	21	74	17	75	10	10	5	73	1.24
54625756--54625894	61	2.3	61	82	6	158	72	5	12	9	1.25
54625810--54625885	35	2.2	35	80	4	82	76	6	9	7	1.16
54626070--54626102	17	1.9	17	93	0	57	27	18	30	24	1.98
54628826--54628855	14	2.1	15	93	6	53	40	0	0	60	0.97
54636774--54636836	3	20.7	3	77	3	63	58	9	0	31	1.30
54636774--54636835	18	3.6	18	89	4	83	58	9	0	32	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54636774--54636825	6	8.7	6	95	0	86	55	11	0	32	1.36
54638486--54638872	132	2.9	132	89	0	569	24	25	20	29	1.99
54638593--54638773	44	4.1	44	65	11	100	24	24	20	29	1.99
54650975--54651032	12	4.4	14	81	14	54	70	0	3	25	1.03
54651001--54651032	3	10.7	3	100	0	64	68	0	0	31	0.90
54653204--54653242	9	4.3	9	96	0	69	53	10	2	33	1.48
54657611--54657655	20	2.3	20	88	3	65	42	0	2	55	1.12
54667618--54667712	43	2.2	43	92	0	163	38	12	24	24	1.90
54669842--54669894	19	2.6	21	82	11	58	22	1	24	50	1.59
54674227--54674262	13	2.8	13	82	0	54	38	8	19	33	1.82

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   207   208