genome.fa.s9.2.7.7.80.10.50.1000.120.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  120  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)
40796423--40796472	23	2.2	23	85	7	66	30	0	2	68	1.01
40796536--40796569	11	3.1	11	95	0	59	44	14	0	41	1.45
40796739--40796854	51	2.3	52	80	7	132	31	6	6	56	1.48
40799368--40799401	5	6.6	5	86	6	50	20	0	2	76	0.92
40801156--40801195	21	1.9	21	89	0	62	25	5	42	27	1.75
40807659--40807686	2	14.0	2	100	0	56	0	50	0	50	1.00
40811928--40811966	2	20.0	2	94	5	71	48	0	0	51	1.00
40816361--40816404	20	2.1	21	84	12	56	45	9	11	34	1.72
40817711--40817751	10	3.9	11	78	9	50	73	4	0	21	1.02
40817873--40818337	153	3.1	150	85	9	606	29	10	9	51	1.67
40818438--40818845	153	2.6	155	85	5	587	30	9	8	51	1.63
40821988--40822053	9	7.2	9	86	10	89	39	28	10	21	1.86
40821988--40822061	20	4.0	20	85	7	95	39	29	9	21	1.85
40825506--40825545	20	2.1	18	86	13	53	25	15	2	57	1.50
40834409--40834517	41	2.7	41	89	0	155	26	21	25	26	1.99
40839293--40839335	15	2.8	16	82	7	61	53	16	18	11	1.72
40839299--40839334	15	2.4	15	95	0	63	55	13	22	8	1.65
40840673--40841065	50	7.9	50	85	5	526	31	21	20	26	1.98
40840664--40841398	150	4.9	150	75	7	604	32	22	20	24	1.98
40840673--40841359	50	13.9	49	75	9	506	31	22	20	24	1.98
40840661--40841447	100	7.9	99	86	3	833	32	22	20	24	1.98
40841127--40841398	50	5.5	50	70	8	216	33	25	18	22	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40843139--40843178	20	2.1	18	86	13	53	25	15	2	57	1.50
40843957--40843981	2	12.5	2	100	0	50	52	0	0	48	1.00
40843973--40844011	18	2.2	18	86	9	53	69	0	2	28	1.02
40844804--40845016	89	2.5	87	80	4	234	40	21	9	28	1.85
40845328--40845363	19	1.9	18	88	5	54	25	2	0	72	0.98
40845303--40845397	48	2.0	48	85	4	129	31	6	2	60	1.34
40845329--40845427	9	10.6	9	69	12	65	27	4	2	66	1.20
40845292--40845409	49	2.4	47	79	9	121	28	5	3	61	1.35
40845386--40845444	18	3.2	19	81	11	61	28	3	1	66	1.18
40845535--40845731	89	2.2	91	82	1	254	31	9	21	37	1.85
40847918--40847995	11	6.8	12	76	19	60	2	23	3	70	1.16
40849563--40849822	18	14.1	18	70	16	124	45	10	11	32	1.74
40849565--40849628	19	3.5	17	80	16	58	42	9	12	35	1.75
40849694--40849759	17	3.6	17	76	11	60	43	9	9	37	1.68
40849721--40849758	20	1.9	20	88	0	58	39	10	10	39	1.74
40849757--40849822	17	3.8	17	82	7	87	53	10	12	24	1.69
40849836--40849905	17	4.2	16	75	10	70	35	11	14	38	1.82
40849836--40849905	16	4.3	15	72	16	59	35	11	14	38	1.82
40849843--40849906	33	1.9	34	90	3	103	34	12	15	37	1.85
40849928--40849980	28	1.9	28	92	3	90	35	7	13	43	1.72
40849959--40850007	17	2.8	17	82	11	64	44	10	16	28	1.80
40851315--40851481	29	5.7	28	78	11	131	40	5	22	32	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40851382--40851498	30	3.9	30	81	10	98	41	4	22	32	1.73
40851693--40852050	75	4.7	72	80	11	321	36	22	16	24	1.94
40851693--40852047	79	4.7	75	82	9	350	35	22	16	25	1.95
40852923--40852981	14	4.1	14	80	10	66	0	5	8	86	0.70
40852923--40852981	17	3.6	16	80	8	64	0	5	8	86	0.70
40852933--40852988	28	2.0	28	92	0	94	0	1	14	83	0.72
40852933--40852983	17	3.0	17	85	5	68	0	1	11	86	0.66
40852923--40852981	11	5.4	11	83	4	66	0	5	8	86	0.70
40858692--40858828	18	7.8	17	73	19	104	43	9	13	32	1.77
40858694--40858954	18	13.9	19	70	18	97	43	9	12	34	1.76
40858676--40858771	38	2.5	37	85	8	113	43	9	12	34	1.75
40858692--40858773	37	2.3	34	82	14	101	42	8	14	34	1.76
40858823--40858861	17	2.2	17	86	4	51	41	5	5	48	1.47
40858889--40858955	17	3.7	18	86	11	93	52	10	13	23	1.71
40858906--40858999	45	2.1	44	84	9	120	47	12	12	26	1.78
40858925--40858978	27	2.0	27	85	3	72	46	14	11	27	1.79
40858860--40859005	64	2.3	63	81	9	163	45	12	11	30	1.77
40858966--40859037	17	4.3	17	74	8	67	37	11	11	40	1.76
40858953--40859038	17	4.9	17	69	18	61	39	11	10	38	1.76
40858951--40859040	37	2.6	35	84	7	121	38	11	11	38	1.76
40859095--40859140	17	2.6	17	83	12	58	45	6	17	30	1.73
40859506--40859535	16	1.9	16	93	6	53	60	0	3	36	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40859509--40859552	20	2.2	20	84	11	56	63	2	2	31	1.19
40859932--40859957	13	2.0	13	100	0	52	0	15	61	23	1.33
40859975--40860006	14	2.2	15	94	5	57	0	21	0	78	0.76
40859973--40860020	21	2.3	21	88	0	69	0	20	0	79	0.74
40859973--40860026	11	5.1	11	82	6	67	0	22	0	77	0.76
40859973--40860032	21	2.9	21	80	9	68	0	23	0	76	0.78
40860291--40860347	24	2.3	26	75	9	64	5	12	14	68	1.37
40860557--40860695	30	4.7	30	81	10	144	41	2	23	33	1.66
40860550--40860717	59	2.9	57	76	12	162	39	4	24	32	1.74
40860602--40860717	30	3.9	28	81	7	106	39	3	24	32	1.72
40867193--40867230	6	6.2	6	85	14	51	13	5	0	81	0.85
40873878--40873902	12	2.1	12	100	0	50	40	40	20	0	1.52
40886229--40886442	106	2.0	106	100	0	428	36	6	20	36	1.78
40889555--40889625	26	2.8	26	82	6	92	36	22	23	16	1.94
40889396--40889640	25	9.9	27	67	14	102	33	19	25	21	1.96
40895292--40895344	20	2.7	20	75	13	56	18	24	3	52	1.62
40896040--40896164	20	6.3	20	65	4	65	37	18	32	11	1.86
40896120--40896357	20	11.9	19	65	11	102	41	15	29	13	1.86
40896051--40896360	40	7.8	40	78	7	247	40	16	29	14	1.87
40896171--40896347	60	3.0	58	70	12	151	41	16	28	13	1.86
40908927--40908977	15	2.8	20	69	27	58	23	21	17	37	1.94
40912933--40912971	12	3.2	12	85	0	51	20	23	5	51	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40913220--40913360	50	2.6	55	81	9	168	25	26	18	29	1.98
40918687--40918835	25	6.0	25	71	5	104	19	26	18	35	1.95
40918687--40918829	75	1.9	75	84	2	189	18	26	18	35	1.95
40918846--40918932	25	3.5	24	75	9	77	20	25	22	31	1.98
40923424--40923469	22	2.1	22	84	8	58	43	2	4	50	1.34
40923717--40923761	20	2.1	21	88	8	65	44	2	6	46	1.42
40923753--40923790	18	2.2	18	85	4	51	52	2	2	42	1.29
40930232--40930325	18	5.4	18	83	8	106	30	8	23	37	1.85
40930265--40930325	9	6.8	9	69	0	50	29	9	22	37	1.87
40933003--40933045	22	2.0	22	100	0	86	37	13	25	23	1.92
40935819--40935866	23	2.1	23	84	3	62	43	16	12	27	1.84
40938179--40938210	5	6.2	5	92	7	55	78	0	0	21	0.76
40938182--40938214	16	2.1	15	94	5	57	78	0	0	21	0.75
40938179--40938214	11	3.4	11	88	3	56	77	0	0	22	0.76
40938461--40938519	29	2.0	30	86	3	84	35	8	5	50	1.55
40942764--40942826	30	2.1	30	93	0	108	22	3	17	57	1.54
40943470--40943513	18	2.4	18	88	3	61	2	54	0	43	1.12
40943809--40943834	11	2.4	11	100	0	52	23	0	15	61	1.33
40946138--40946176	20	2.0	20	94	0	69	48	0	2	48	1.15
40946259--40946335	14	5.0	15	71	20	52	42	15	9	32	1.78
40946275--40946314	20	2.0	20	90	0	62	50	12	10	27	1.72
40946263--40946329	34	1.9	35	90	3	109	46	13	8	31	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40946298--40946337	14	2.9	14	84	0	53	42	17	7	32	1.77
40949079--40949115	9	4.1	9	92	0	65	45	13	10	29	1.77
40949666--40949691	13	2.0	13	100	0	52	38	7	0	53	1.30
40950210--40950235	5	5.2	5	100	0	52	19	19	19	42	1.90
40951008--40951045	20	1.9	20	84	10	51	44	5	0	50	1.24
40953964--40954021	30	1.9	30	93	6	100	44	0	22	32	1.53
40956488--40956558	26	2.8	25	81	8	90	47	7	0	45	1.30
40956556--40956588	13	2.5	13	100	0	66	69	18	6	6	1.30
40956630--40956696	27	2.5	27	92	0	107	28	29	25	16	1.97
40956740--40956884	4	36.0	4	75	19	101	71	0	28	0	0.87

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