genome.fa.s9.2.7.7.80.10.50.1000.139.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: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  70713020

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   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   

This is table  139  of  226  ( 27023 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)
46373295--46373357	27	2.3	27	83	5	65	30	25	7	36	1.84
46373383--46373684	53	5.7	53	79	2	277	26	21	9	41	1.84
46373383--46373669	106	2.7	105	81	5	337	26	21	10	41	1.85
46373532--46373661	26	4.9	26	70	2	98	27	22	9	40	1.84
46373566--46373684	26	4.5	27	73	5	91	26	21	9	42	1.83
46373383--46373679	159	1.9	159	84	1	407	26	21	10	41	1.85
46375332--46375431	27	3.7	27	82	5	121	27	22	15	36	1.93
46375544--46375638	47	2.0	47	83	6	118	27	25	14	32	1.95
46388158--46388183	13	2.0	13	100	0	52	23	15	15	46	1.83
46388534--46388573	20	2.0	20	85	4	55	62	0	2	35	1.09
46388618--46388713	33	2.8	35	72	20	87	46	3	1	48	1.24
46388900--46388950	13	3.9	13	75	10	59	39	23	5	31	1.79
46388899--46388950	26	2.0	27	84	3	70	40	23	5	30	1.78
46393428--46393527	26	3.8	26	73	5	94	22	12	33	33	1.90
46405264--46405321	22	2.8	22	80	12	70	60	0	0	39	0.97
46412460--46412506	16	2.8	16	87	9	58	72	0	2	25	0.96
46414108--46414137	3	10.0	3	92	0	51	63	0	3	33	1.11
46415521--46415546	3	8.7	3	100	0	52	34	0	0	65	0.93
46416114--46416166	2	26.5	2	96	0	97	50	1	0	47	1.12
46416289--46416327	16	2.5	15	84	8	51	43	0	12	43	1.42
46423838--46423929	32	2.8	32	85	1	112	22	36	19	20	1.95
46427739--46427778	20	2.0	20	100	0	80	45	30	5	20	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46431078--46431131	26	2.1	26	100	0	108	22	20	24	33	1.97
46433471--46433510	19	2.1	19	85	0	53	20	17	35	27	1.95
46433490--46433677	41	4.6	41	91	4	290	16	21	32	29	1.95
46434120--46434171	20	2.6	20	82	11	70	15	0	48	36	1.45
46434115--46434173	13	4.3	14	77	18	61	16	0	44	38	1.48
46434115--46434173	7	8.6	7	78	16	61	16	0	44	38	1.48
46434231--46434270	7	5.7	7	96	0	71	2	0	57	40	1.12
46434213--46434278	7	9.4	7	84	0	60	12	0	48	39	1.40
46434210--46434277	21	3.2	21	80	2	73	10	0	50	39	1.37
46434852--46434905	27	2.0	27	100	0	108	55	3	18	22	1.58
46439302--46439349	22	2.0	23	84	11	62	54	2	2	41	1.24
46439398--46439686	43	6.8	43	87	2	377	20	15	34	29	1.94
46439362--46439684	128	2.5	129	87	2	445	20	14	33	30	1.93
46441971--46442043	36	2.0	36	100	0	146	21	8	36	32	1.83
46444047--46444191	63	2.3	63	80	3	157	23	21	28	26	1.99
46444851--46444900	22	2.3	22	86	6	66	14	12	20	54	1.71
46449199--46449260	25	2.4	25	86	7	81	40	1	4	53	1.32
46449337--46449413	38	2.0	38	95	5	138	50	6	12	29	1.66
46451260--46451304	17	2.8	17	83	12	51	35	2	6	55	1.38
46451852--46451891	19	2.1	19	86	9	55	55	0	0	45	0.99
46456919--46456955	2	18.5	2	100	0	74	48	0	0	51	1.00
46459588--46459616	15	1.9	15	100	0	58	34	0	10	55	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46462566--46462666	31	3.3	31	87	0	139	21	3	38	35	1.72
46469295--46469425	45	2.9	45	85	7	176	25	19	9	44	1.82
46473125--46473168	21	2.1	21	86	0	61	34	29	6	29	1.83
46479778--46479995	60	3.6	60	88	0	319	33	19	16	31	1.94
46479769--46480036	90	3.0	90	81	1	286	32	18	16	32	1.93
46479774--46480036	30	8.8	30	82	1	213	33	19	15	32	1.93
46483266--46483369	35	3.0	35	82	2	129	33	15	23	27	1.95
46487286--46487338	3	17.7	3	100	0	106	0	32	0	67	0.91
46496471--46496528	22	2.6	22	88	0	80	44	13	17	24	1.85
46498589--46498646	18	3.3	18	82	4	64	72	5	3	18	1.18
46519930--46520079	43	3.5	43	87	1	212	46	3	23	26	1.68
46524426--46524495	33	2.1	33	84	5	88	41	12	24	21	1.88
46531932--46531970	20	2.0	20	89	0	60	38	7	12	41	1.72
46532066--46532421	20	17.8	20	69	8	206	36	6	16	40	1.74
46532511--46532560	20	2.5	21	84	12	61	36	4	20	40	1.71
46532596--46532649	21	2.6	21	88	2	74	51	1	14	31	1.53
46532613--46532670	20	2.8	20	86	2	71	43	0	18	37	1.51
46534979--46535041	29	2.2	29	82	0	72	19	25	28	26	1.98
46537543--46537706	20	8.2	20	74	8	127	39	5	17	38	1.73
46540703--46540801	20	4.9	20	73	2	72	42	3	17	37	1.64
46540852--46540905	20	2.7	20	85	0	72	48	3	11	37	1.57
46540852--46540999	40	3.7	39	74	9	111	42	6	12	39	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46541039--46541092	21	2.7	20	80	5	63	44	5	11	38	1.63
46544164--46544208	15	3.2	13	77	22	54	51	2	0	46	1.13
46544177--46544219	19	2.2	20	84	12	54	48	2	2	46	1.27
46547716--46547758	20	2.2	20	82	0	50	48	0	9	41	1.35
46554237--46554298	31	2.0	31	100	0	124	19	19	32	29	1.96
46557146--46557183	19	2.0	19	85	10	51	57	7	2	31	1.41
46568292--46568371	39	2.1	39	100	0	160	21	27	10	41	1.85
46571403--46571446	23	2.0	22	83	12	56	61	4	18	15	1.50
46574807--46574939	27	5.0	27	88	1	178	18	17	22	42	1.89
46575620--46575661	12	3.5	12	78	12	50	19	42	0	38	1.51
46575797--46575845	24	2.0	24	100	0	98	34	12	16	36	1.86
46576474--46576523	18	3.0	17	83	11	59	72	10	12	6	1.28
46581185--46581344	28	5.7	28	85	0	176	28	20	25	26	1.99
46581186--46581342	84	1.9	84	84	0	215	28	20	24	26	1.99
46581732--46581864	27	5.0	27	87	3	171	17	19	22	40	1.91
46582817--46582864	23	2.1	23	100	0	96	58	16	8	16	1.61
46585029--46585221	38	5.1	38	84	2	217	15	16	30	37	1.90
46595532--46595609	40	2.0	40	89	0	120	52	3	24	19	1.62
46601799--46601873	37	2.0	37	100	0	150	32	13	24	30	1.93
46607131--46607194	30	2.1	29	81	13	76	43	14	3	39	1.61
46609208--46609297	38	2.4	38	78	0	99	36	14	17	31	1.90
46609228--46609308	38	2.1	38	88	0	117	33	13	20	32	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46612363--46612394	17	1.9	16	93	6	55	40	6	21	31	1.78
46628907--46629104	51	3.9	50	77	4	218	31	28	16	23	1.96
46628915--46629100	101	1.8	99	84	5	239	32	27	16	23	1.95
46642660--46642865	39	5.3	38	84	4	225	18	32	16	32	1.94
46642749--46642820	19	3.8	18	71	12	54	13	31	19	34	1.91
46642671--46642865	76	2.5	78	84	2	259	18	32	16	32	1.94
46642776--46642840	20	3.3	20	71	4	69	13	38	18	29	1.89
46648127--46648544	27	15.6	27	85	1	525	39	21	20	18	1.93
46661230--46661318	44	2.0	44	86	0	124	56	12	7	23	1.62
46672681--46672946	42	6.3	43	88	2	376	25	31	18	24	1.98
46672681--46672921	85	2.8	85	94	0	403	25	30	18	24	1.98
46675436--46675508	33	2.2	33	97	0	137	54	12	8	24	1.64
46677424--46677520	28	3.5	27	72	16	74	36	40	2	21	1.65
46677767--46677869	29	3.6	28	76	8	100	34	40	0	24	1.55
46677790--46677837	14	3.4	14	91	2	78	33	41	0	25	1.55
46677801--46677862	21	3.0	20	79	6	61	35	41	0	22	1.54
46678242--46678332	41	2.2	41	94	0	155	28	28	21	20	1.99
46678368--46678503	40	3.4	40	80	1	148	25	21	15	37	1.93
46687434--46687472	20	1.9	21	89	5	62	43	7	0	48	1.31
46693420--46693600	41	4.4	41	89	2	240	38	12	25	23	1.90
46694600--46694642	22	2.0	21	82	13	52	55	0	4	39	1.20
46695834--46695885	26	2.0	26	100	0	104	42	7	11	38	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
46701856--46701906	26	2.0	26	85	11	70	41	5	9	43	1.62
46703974--46704025	26	2.0	26	88	0	77	42	9	11	36	1.74
46705826--46705877	26	2.0	26	92	0	86	44	9	11	34	1.73
46707679--46707730	26	2.0	26	92	0	86	44	9	11	34	1.73
46709531--46709582	26	2.0	26	92	0	86	44	9	11	34	1.73
46711460--46711511	26	2.0	26	96	0	95	44	7	9	38	1.66
46720545--46720586	3	14.0	3	100	0	84	66	0	0	33	0.92
46720548--46720614	6	11.2	6	88	0	53	58	5	0	35	1.23
46721595--46721632	14	2.4	17	87	12	55	52	0	0	47	1.00
46721622--46721672	20	2.6	19	82	14	59	52	1	0	45	1.12

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   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226