genome.fa.s4.2.7.7.80.10.50.1000.94.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  94  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)
30106246--30106289	20	2.2	20	84	4	54	38	4	45	11	1.61
30109508--30109564	28	2.0	28	89	0	87	33	21	22	22	1.97
30109795--30109883	32	2.8	31	79	3	88	37	22	20	20	1.95
30110138--30110205	27	2.6	27	78	2	75	23	22	19	35	1.96
30110162--30110359	27	7.3	27	79	6	197	18	18	20	42	1.89
30115315--30115372	25	2.3	25	87	0	80	27	17	18	36	1.94
30118568--30118600	17	2.0	17	88	5	50	51	6	0	42	1.26
30123010--30123133	45	2.7	46	86	6	173	22	20	13	42	1.87
30125546--30125756	73	2.8	74	80	9	232	41	17	4	36	1.69
30125546--30125796	76	3.4	74	77	13	230	41	17	4	36	1.71
30130050--30130352	150	2.0	151	92	1	509	41	8	18	30	1.81
30130891--30130955	19	3.4	18	87	4	85	21	24	20	33	1.97
30131343--30131390	14	3.4	14	75	11	53	54	0	22	22	1.45
30133818--30133870	16	3.3	16	91	0	88	41	3	32	22	1.72
30134102--30134148	18	2.6	18	90	6	69	57	0	0	42	0.98
30134080--30134312	121	1.9	121	95	1	423	51	3	0	44	1.23
30134223--30134269	18	2.6	18	90	6	69	57	0	0	42	0.98
30134411--30134443	14	2.3	15	89	5	50	75	6	0	18	1.00
30136113--30136216	49	2.1	49	87	1	147	51	10	8	28	1.66
30138896--30138940	9	4.7	10	76	18	51	37	0	0	62	0.96
30138984--30139013	16	1.9	15	93	6	51	33	3	0	63	1.11
30139398--30139422	10	2.5	10	100	0	50	44	28	8	20	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30139676--30139713	13	3.0	13	81	18	53	44	15	0	39	1.47
30148702--30148732	16	1.9	16	93	0	53	58	3	0	38	1.15
30151861--30151914	27	2.0	26	85	3	72	50	1	1	46	1.23
30159681--30159955	25	11.1	25	71	15	153	18	25	21	34	1.96
30159704--30159753	26	2.0	25	92	4	82	18	22	24	36	1.95
30167019--30167056	14	2.5	15	87	8	51	2	23	0	73	0.95
30167028--30167065	19	2.0	19	85	10	51	0	23	0	76	0.79
30172209--30172251	13	3.3	13	96	0	77	34	46	18	0	1.50
30174565--30174589	9	2.8	9	100	0	50	12	44	24	20	1.85
30179558--30179592	16	2.1	17	94	5	63	40	0	48	11	1.39
30179615--30181046	710	2.0	716	83	6	1816	36	14	13	35	1.85
30194292--30194354	26	2.4	26	86	0	90	38	11	12	38	1.79
30208373--30208623	40	6.3	40	80	3	220	38	15	26	19	1.92
30208388--30208496	20	5.4	20	65	8	60	33	18	28	20	1.96
30208373--30208623	80	3.1	80	78	6	258	38	15	26	19	1.92
30208391--30208625	120	2.0	120	79	5	260	37	15	26	20	1.92
30212984--30213226	50	4.9	50	90	0	342	27	20	30	21	1.98
30219667--30219825	21	7.1	22	72	18	89	36	9	2	51	1.48
30219863--30219921	30	2.0	29	83	3	73	30	3	5	61	1.34
30226367--30226405	15	2.7	14	96	4	69	66	2	12	17	1.35
30235200--30235231	9	3.6	9	100	0	64	81	0	9	9	0.88
30236192--30236252	24	2.5	24	86	0	86	34	9	26	29	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30236590--30237037	46	9.3	46	80	9	475	28	19	25	26	1.99
30236560--30237037	97	4.9	97	86	6	691	28	19	25	26	1.99
30238809--30238935	45	2.8	44	81	11	123	40	7	2	48	1.45
30238806--30238935	24	5.7	21	73	19	93	40	7	2	50	1.44
30238929--30238974	22	2.1	22	84	11	60	34	8	2	54	1.43
30239003--30239048	15	3.1	15	74	20	51	28	2	6	63	1.31
30239003--30239062	30	2.0	30	83	6	77	28	3	5	63	1.31
30239469--30239525	25	2.3	25	80	14	64	28	7	3	61	1.39
30239476--30239524	24	1.9	25	84	12	64	28	6	4	61	1.38
30240439--30240517	22	3.6	22	85	0	113	29	13	26	30	1.94
30243081--30243284	102	2.0	100	92	4	338	39	15	17	27	1.90
30251887--30251993	43	2.5	43	84	0	124	33	25	14	27	1.94
30252340--30252807	235	2.0	233	97	0	873	32	17	19	30	1.95
30257309--30257338	15	2.0	15	93	0	51	43	30	0	26	1.55
30257697--30257772	40	1.9	40	88	0	116	34	21	22	22	1.97
30257818--30257922	39	2.6	41	83	8	137	20	20	19	40	1.91
30260714--30260739	12	2.2	12	100	0	52	30	15	34	19	1.93
30262421--30262724	27	11.3	27	86	2	373	44	18	16	20	1.87
30268009--30268034	3	8.7	3	100	0	52	34	30	0	34	1.58
30279071--30279187	40	2.9	39	87	6	164	45	25	17	11	1.82
30279166--30279207	21	2.0	21	100	0	84	42	14	23	19	1.87
30279126--30279247	61	2.0	60	87	1	172	42	22	20	14	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30279186--30279272	39	2.2	40	87	4	131	37	28	20	12	1.89
30279086--30279272	100	1.9	101	85	1	259	41	25	19	13	1.88
30280624--30280873	40	6.2	41	82	5	294	33	16	29	20	1.95
30280604--30280869	121	2.2	121	82	3	320	34	16	28	20	1.95
30285215--30285239	2	12.5	2	100	0	50	48	0	0	52	1.00
30288065--30288451	88	4.4	88	86	2	528	28	24	19	27	1.99
30288065--30288445	174	2.2	174	88	1	566	28	24	19	27	1.99
30303030--30303071	21	2.0	22	81	13	52	45	28	7	19	1.76
30307813--30307898	40	2.2	40	95	0	154	26	11	15	46	1.80
30308116--30308189	24	3.2	24	79	11	91	41	12	14	31	1.83
30308098--30308189	45	2.0	45	87	0	130	40	11	17	30	1.86
30308946--30308985	21	1.9	21	89	0	62	17	12	17	52	1.74
30320258--30320283	7	3.7	7	100	0	52	15	0	0	84	0.62
30321130--30321188	24	2.5	23	78	5	55	30	5	6	57	1.46
30321322--30321349	13	2.2	13	100	0	56	14	7	0	78	0.95
30333646--30333697	25	2.1	24	92	3	86	26	25	15	32	1.95
30341597--30341638	22	2.0	21	86	13	59	52	14	11	21	1.73
30345915--30345958	20	2.2	20	83	0	52	54	9	6	29	1.58
30347390--30347574	51	3.7	50	82	3	228	25	17	27	29	1.98
30347400--30347584	102	1.8	101	88	3	264	27	17	26	28	1.98
30352471--30352513	22	1.9	23	85	4	61	23	18	11	46	1.82
30367253--30367297	18	2.4	19	81	7	56	17	6	26	48	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30370502--30370565	32	2.0	33	82	14	80	15	17	1	65	1.35
30372085--30372159	37	2.0	37	100	0	150	38	2	16	42	1.62
30376042--30376075	17	2.0	17	94	0	59	17	32	17	32	1.94
30376642--30376798	45	3.5	45	88	5	221	35	27	17	19	1.95
30384236--30384309	29	2.5	29	82	4	85	24	13	13	48	1.78
30385042--30385081	20	2.0	20	90	9	64	47	2	0	50	1.14
30386729--30386817	13	6.7	13	71	16	67	40	1	17	40	1.57
30386764--30386828	27	2.5	26	83	16	80	36	0	20	43	1.52
30386724--30386800	40	1.9	40	94	0	136	42	1	16	38	1.57
30386764--30386828	13	4.9	13	76	10	60	36	0	20	43	1.52
30390237--30390270	3	11.3	3	100	0	68	67	0	32	0	0.91
30393553--30393578	13	2.0	13	100	0	52	30	30	7	30	1.85
30399856--30399900	22	2.0	22	83	8	56	42	4	0	53	1.21
30409104--30409282	27	6.6	27	72	7	103	20	26	23	29	1.99
30409212--30409309	27	3.7	26	79	5	97	18	30	21	29	1.97
30411665--30411709	7	7.0	7	82	12	53	75	11	13	0	1.05
30411651--30411721	25	2.7	26	89	6	108	76	11	12	0	1.03
30425202--30425235	4	8.2	4	87	6	50	76	0	2	20	0.92
30425204--30425245	17	2.4	18	96	4	77	78	0	4	16	0.91
30428019--30428325	20	15.1	20	69	8	120	38	18	29	13	1.89
30428020--30428162	40	3.6	40	87	0	205	37	18	32	11	1.88
30428138--30428187	25	2.0	25	100	0	100	32	16	36	16	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30428100--30428225	65	1.9	65	90	0	198	38	18	30	13	1.89
30428060--30428267	105	2.0	105	89	0	317	38	18	28	13	1.89
30428167--30428345	40	4.5	39	86	3	241	39	18	26	15	1.90
30428020--30428307	145	2.0	145	89	1	443	38	18	29	12	1.88
30432448--30432476	12	2.5	12	94	5	51	37	10	0	51	1.36
30435601--30435630	3	10.0	3	100	0	60	33	33	0	33	1.58
30440431--30440519	27	3.3	27	85	0	97	38	11	25	24	1.89
30457902--30457955	25	2.1	26	83	10	67	31	3	1	62	1.23
30466856--30466932	27	2.9	27	76	0	82	15	16	32	35	1.91
30469396--30469458	26	2.4	26	86	0	81	34	7	14	42	1.75

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