genome.fa.s9.2.7.7.80.10.50.1000.112.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  112  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)
38440081--38440114	11	3.2	11	83	8	52	29	11	32	26	1.92
38443216--38443244	15	1.9	15	100	0	58	41	13	20	24	1.89
38447907--38447996	45	2.0	45	82	4	110	36	14	11	37	1.82
38452044--38452097	27	2.0	27	92	0	90	27	27	9	35	1.87
38456799--38456896	52	1.9	51	93	2	169	40	13	22	23	1.89
38456847--38456989	29	4.9	29	87	4	173	39	14	27	18	1.90
38459270--38459306	9	4.1	9	92	0	65	29	10	13	45	1.77
38459765--38459791	14	1.9	14	100	0	54	25	7	22	44	1.79
38460636--38460665	15	2.0	15	93	0	51	6	23	20	50	1.71
38463947--38464332	27	14.3	27	81	5	354	41	17	17	23	1.89
38464527--38464633	26	4.1	26	82	0	124	19	19	25	35	1.95
38464527--38464633	52	2.1	52	85	0	142	19	19	25	35	1.95
38464741--38464821	30	2.7	30	77	7	92	22	24	23	29	1.99
38465042--38465088	19	2.5	18	82	6	58	19	0	12	68	1.21
38466662--38466724	30	2.1	30	96	0	117	20	9	38	31	1.85
38471792--38472150	27	13.3	27	79	3	330	42	19	16	21	1.89
38472340--38472446	52	2.1	52	85	3	144	19	20	23	36	1.95
38472340--38472446	26	4.1	26	79	4	126	19	20	23	36	1.95
38477915--38477970	28	2.0	28	92	0	94	23	16	8	51	1.72
38484889--38484946	2	29.0	2	100	0	116	50	0	0	50	1.00
38488810--38488868	30	2.0	30	86	0	82	22	25	27	25	2.00
38493691--38493763	6	12.7	6	81	5	71	0	21	1	76	0.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38501292--38501320	12	2.5	12	94	5	51	6	17	0	75	1.01
38509770--38509796	2	13.5	2	100	0	54	51	0	48	0	1.00
38519351--38519690	30	11.4	30	76	8	225	39	13	23	23	1.90
38519374--38519451	29	2.6	29	86	11	113	44	12	23	19	1.84
38519470--38519694	119	1.9	119	82	3	283	39	12	24	24	1.90
38519559--38519630	29	2.4	30	88	4	110	38	9	30	20	1.85
38519351--38519695	89	3.9	88	75	7	320	39	13	24	23	1.90
38519351--38519685	179	1.9	179	90	0	535	39	13	23	23	1.90
38520486--38520734	50	4.8	50	86	3	318	20	30	23	25	1.99
38520485--38520734	100	2.4	103	89	5	371	20	30	23	25	1.99
38525740--38525989	100	2.4	104	88	5	364	22	30	22	25	1.99
38525740--38525989	50	4.8	51	84	5	299	22	30	22	25	1.99
38536920--38536965	25	1.9	24	82	8	58	19	17	10	52	1.74
38541326--38541368	16	2.7	16	82	7	52	55	2	0	41	1.12
38557246--38557542	149	2.0	149	91	0	486	39	17	21	20	1.92
38558603--38558743	54	2.6	54	83	4	133	20	30	28	20	1.98
38558641--38558754	54	2.1	54	88	0	165	21	26	29	22	1.99
38564063--38564103	20	2.1	20	86	4	57	60	9	12	17	1.57
38581950--38581979	15	2.0	15	100	0	60	13	20	26	40	1.89
38592574--38592684	54	2.1	54	100	0	222	36	3	21	37	1.71
38592584--38592672	26	3.3	26	73	11	99	37	3	22	37	1.71
38594118--38594143	12	2.2	12	100	0	52	23	38	30	7	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38607565--38607688	50	2.5	51	80	7	146	21	26	24	27	1.99
38610175--38610305	46	2.8	46	90	0	190	36	1	9	51	1.44
38612232--38612322	41	2.2	42	88	2	130	31	23	12	32	1.91
38613489--38613951	23	19.6	24	71	11	192	41	17	13	28	1.87
38613561--38613948	23	16.5	23	73	4	290	42	16	13	27	1.86
38613504--38613948	71	6.3	70	86	2	586	42	17	13	27	1.86
38613504--38613948	141	3.1	141	91	1	694	42	17	13	27	1.86
38613581--38613950	48	7.8	49	71	13	168	42	16	13	27	1.86
38614674--38614771	28	3.5	28	87	0	133	31	24	12	31	1.92
38615946--38616383	235	1.9	234	91	1	716	29	13	22	34	1.92
38619971--38620005	13	2.7	13	95	0	61	60	5	34	0	1.21
38621325--38621396	33	2.1	34	89	2	110	40	6	12	40	1.70
38624489--38624777	27	10.7	27	85	1	330	43	20	18	17	1.88
38624486--38624760	81	3.4	80	84	1	370	43	21	18	17	1.88
38624972--38625023	26	2.0	26	88	0	77	11	23	25	40	1.88
38625138--38625223	28	3.0	28	81	6	109	25	26	20	26	1.99
38625132--38625252	28	3.9	31	76	15	108	24	26	22	26	2.00
38630597--38630636	20	2.0	20	100	0	80	35	20	15	30	1.93
38631105--38631138	15	2.3	15	89	0	50	26	29	8	35	1.87
38632386--38632709	162	2.0	161	94	1	569	37	22	7	32	1.83
38634493--38634587	41	2.3	41	88	0	136	31	17	16	33	1.93
38635854--38635962	51	2.1	51	86	3	148	29	3	53	13	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38636027--38636146	19	6.3	19	70	11	59	32	1	1	64	1.13
38636099--38636142	22	2.0	23	90	4	72	34	0	2	63	1.07
38636098--38636156	22	2.8	21	80	14	68	33	0	3	62	1.12
38636049--38636164	51	2.2	53	80	8	132	33	1	1	62	1.15
38638617--38638643	13	2.1	13	100	0	54	48	0	14	37	1.45
38638856--38638904	23	2.1	23	92	0	80	36	24	2	36	1.67
38640598--38640637	6	6.7	6	94	0	62	10	0	57	32	1.32
38640991--38641052	31	2.0	31	100	0	124	38	9	9	41	1.71
38642240--38643729	575	2.6	551	82	8	1705	38	8	13	39	1.76
38645407--38645438	16	2.0	16	93	0	55	43	9	18	28	1.81
38645806--38645938	50	2.6	51	82	7	164	21	28	23	26	1.99
38651854--38652251	199	2.0	199	91	1	647	27	25	15	31	1.96
38655680--38655725	22	2.1	22	84	8	58	39	4	0	56	1.19
38656009--38656038	13	2.3	13	94	0	51	10	13	20	56	1.65
38686914--38687014	52	1.9	52	95	0	184	26	18	21	32	1.97
38692470--38692529	15	3.8	15	71	16	50	46	23	1	28	1.62
38693999--38694198	50	3.9	50	81	6	215	27	21	28	23	1.99
38694012--38694198	100	1.8	104	82	6	247	26	20	28	23	1.99
38694062--38694257	50	3.9	49	78	6	162	28	20	26	25	1.99
38701693--38701885	50	3.7	50	83	4	215	25	21	29	22	1.99
38708730--38708777	3	16.0	3	100	0	96	33	0	0	66	0.92
38721084--38721143	18	3.3	18	86	6	77	70	0	8	21	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38721085--38721141	19	3.2	18	90	5	80	70	0	8	21	1.14
38726747--38726855	46	2.4	45	81	3	137	46	16	16	20	1.84
38726844--38727059	45	4.8	45	88	1	308	36	18	19	25	1.95
38726843--38727098	90	2.8	90	83	4	320	37	17	20	24	1.94
38727027--38727138	46	2.5	46	83	1	127	45	15	20	18	1.85
38726844--38727098	135	1.9	135	82	4	318	37	18	20	23	1.94
38729761--38729823	25	2.6	25	80	10	76	31	7	3	57	1.43
38730007--38730048	16	2.7	16	82	10	52	28	4	2	64	1.26
38733724--38733763	18	2.2	18	100	0	80	20	35	0	45	1.51
38735489--38735583	47	2.0	48	87	2	138	45	20	21	13	1.85
38736440--38736485	24	1.9	24	90	0	74	36	15	21	26	1.93
38736828--38737667	44	17.9	44	66	15	274	30	20	22	26	1.98
38736966--38737754	44	16.7	47	66	20	278	30	20	22	26	1.98
38736826--38737746	427	2.1	429	88	1	1292	30	20	22	26	1.98
38736818--38737720	143	6.3	143	87	1	1285	30	19	22	26	1.98
38739654--38739678	2	12.5	2	100	0	50	52	0	0	48	1.00
38739699--38739740	16	2.7	16	82	10	52	28	4	2	64	1.26
38744369--38744447	41	1.9	41	89	0	122	27	22	20	29	1.98
38744369--38744482	43	2.7	41	83	2	120	26	22	19	31	1.98
38744994--38745134	7	19.7	7	70	7	50	43	32	0	22	1.58
38745038--38745069	15	2.2	14	94	5	55	37	40	0	21	1.54
38745148--38745197	14	3.6	14	75	2	57	50	28	0	22	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
38745653--38745691	14	2.7	15	84	11	55	46	28	0	25	1.53
38745907--38746007	14	7.2	14	71	15	66	45	33	1	18	1.61
38745975--38746066	22	4.3	22	71	8	64	45	27	2	25	1.65
38746254--38746545	41	7.1	41	85	3	365	30	27	19	22	1.98
38746685--38746710	12	2.2	12	100	0	52	46	23	15	15	1.83
38752010--38752185	87	2.0	87	96	0	325	31	15	11	41	1.83
38756918--38756950	2	16.5	2	100	0	66	48	0	0	51	1.00
38766458--38766489	11	2.9	11	90	0	55	28	6	0	65	1.16
38767001--38767076	32	2.3	33	90	4	118	31	3	21	43	1.71
38767105--38767170	29	2.3	29	86	2	89	31	3	16	48	1.62

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