genome.fa.s9.2.7.7.80.10.50.1000.123.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  123  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)
41574728--41574942	99	2.2	100	83	4	272	28	25	15	30	1.96
41578013--41578270	76	3.4	76	85	0	264	29	22	23	24	1.99
41578025--41578211	36	4.9	40	65	10	120	29	22	23	24	1.99
41583542--41583635	39	2.4	39	83	0	125	45	11	9	32	1.73
41583790--41583828	3	13.0	3	100	0	78	0	33	0	66	0.92
41587203--41587280	35	2.1	36	86	6	104	38	26	15	19	1.91
41595786--41595932	51	2.9	50	85	5	206	34	12	14	39	1.83
41597509--41597625	28	4.2	28	88	1	173	31	25	20	22	1.98
41597733--41597833	26	3.9	26	89	0	148	34	23	22	18	1.96
41597835--41597915	39	2.1	39	100	0	162	30	32	7	29	1.85
41598031--41598318	27	10.7	26	79	5	216	20	20	21	37	1.94
41598041--41598318	54	5.1	54	85	2	362	19	20	21	38	1.94
41598042--41598318	81	3.4	80	84	3	367	19	20	21	38	1.94
41602649--41602760	52	2.2	49	84	4	143	40	4	5	50	1.45
41606265--41606310	23	2.0	23	86	0	65	67	13	0	19	1.23
41606533--41606605	19	3.8	19	96	0	137	36	16	9	36	1.81
41606510--41606605	38	2.4	39	89	6	140	38	16	8	36	1.79
41606866--41607209	45	7.8	44	73	11	197	25	23	21	29	1.99
41606866--41607335	44	10.8	43	72	15	283	26	22	21	29	1.99
41606908--41607352	217	2.0	218	87	2	644	25	23	20	30	1.99
41607692--41607855	44	3.7	44	90	3	242	29	26	17	26	1.97
41609100--41609153	16	3.4	17	73	19	53	0	24	0	75	0.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41609101--41609141	19	2.2	19	86	0	55	0	21	0	78	0.76
41609109--41609159	12	4.2	12	85	12	68	0	19	0	80	0.71
41609100--41609161	24	2.6	23	87	5	88	0	24	0	75	0.80
41609109--41609158	18	2.8	17	85	11	64	0	20	0	80	0.72
41614017--41614072	24	2.2	25	81	6	69	67	16	1	14	1.31
41614286--41614339	19	2.8	19	94	0	99	37	16	9	37	1.81
41614263--41614339	38	1.9	40	87	10	113	38	16	7	36	1.78
41617286--41617398	57	2.0	58	87	5	167	38	19	21	21	1.94
41617288--41617392	29	3.7	29	75	7	99	37	19	21	21	1.95
41617358--41617440	40	2.1	40	90	0	130	30	19	27	22	1.98
41617414--41617514	28	3.6	28	75	15	100	33	16	24	24	1.96
41617398--41617687	57	5.1	57	79	1	296	32	17	25	25	1.97
41617307--41617493	97	1.9	97	86	0	266	34	19	24	21	1.97
41617402--41617486	28	3.0	29	72	16	86	34	18	23	23	1.97
41617499--41617603	29	3.7	29	72	7	79	36	14	23	25	1.93
41617398--41617638	114	2.1	114	85	0	329	33	16	24	25	1.96
41620504--41620542	18	2.2	17	86	13	53	33	0	20	46	1.51
41620760--41620880	23	5.3	23	83	8	167	21	19	27	32	1.97
41620760--41620880	45	2.7	46	88	2	181	21	19	27	32	1.97
41621084--41621131	23	2.0	25	84	8	64	39	0	22	37	1.55
41634472--41634532	30	2.0	30	100	0	122	39	6	32	21	1.79
41638866--41638918	29	1.9	27	85	11	72	7	24	1	66	1.28
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41639902--41639936	18	2.0	17	88	5	52	77	0	2	20	0.90
41639949--41639984	18	2.0	18	89	10	56	69	0	0	30	0.89
41639944--41639986	18	2.5	17	82	14	52	67	2	0	30	1.03
41641911--41642272	100	3.6	99	87	0	472	25	22	21	29	1.99
41641911--41642275	50	7.3	50	66	2	194	25	22	21	29	1.99
41650357--41650388	15	2.1	15	94	0	55	65	15	0	18	1.27
41650395--41650431	13	2.7	14	80	20	51	64	8	5	21	1.40
41650677--41650722	24	1.9	24	82	8	58	54	0	6	39	1.26
41650804--41650828	4	6.2	4	100	0	50	76	0	0	24	0.80
41650839--41650887	2	25.0	2	79	4	55	51	2	4	42	1.32
41650817--41650894	33	2.5	33	81	8	92	52	3	5	38	1.42
41650809--41650887	39	2.0	39	82	0	95	55	3	3	36	1.36
41651199--41651233	17	2.0	17	94	5	61	82	0	0	17	0.66
41651199--41651233	6	6.0	6	93	6	63	82	0	0	17	0.66
41651198--41651275	18	4.4	18	75	10	54	69	1	2	26	1.09
41654061--41654269	42	5.0	42	86	5	271	31	20	22	25	1.98
41654061--41654235	85	2.1	85	91	2	280	33	21	21	24	1.97
41654700--41654795	21	4.4	21	76	7	66	5	41	15	37	1.70
41656896--41657134	25	8.9	25	71	20	128	38	0	18	42	1.56
41656896--41657259	9	40.6	9	68	16	186	35	1	17	44	1.59
41656896--41657196	25	11.2	25	69	21	125	37	0	17	43	1.56
41656965--41657016	19	2.8	19	85	2	70	32	1	19	46	1.61
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41656949--41657184	16	14.8	16	72	16	118	36	0	17	45	1.55
41659375--41659613	115	2.1	115	94	0	415	32	20	18	28	1.96
41660061--41660142	7	12.0	6	78	15	56	46	31	2	19	1.63
41660080--41660140	21	2.9	21	76	9	70	45	34	3	16	1.63
41660061--41660142	14	5.9	13	77	17	67	46	31	2	19	1.63
41660272--41660321	20	2.5	21	83	6	68	48	38	0	14	1.44
41660460--41660522	7	8.9	7	76	8	56	36	46	1	15	1.56
41661119--41661271	72	2.1	72	84	2	200	31	24	21	22	1.98
41661119--41661300	72	2.6	72	80	3	172	26	23	23	25	2.00
41663629--41663673	20	2.2	20	88	7	65	64	4	0	31	1.13
41676098--41676138	21	2.0	21	85	0	55	19	21	29	29	1.98
41677267--41677319	28	1.9	27	84	3	70	24	0	9	66	1.21
41677648--41677702	2	27.5	2	89	7	85	49	0	3	47	1.19
41678406--41678441	2	18.0	2	94	0	63	47	0	0	52	1.00
41724822--41725104	65	4.4	63	81	4	228	33	14	14	37	1.87
41724839--41725043	63	3.2	63	81	13	215	32	13	16	37	1.87
41724821--41725104	128	2.2	128	79	5	295	33	14	14	37	1.87
41729435--41729522	44	2.0	44	100	0	176	54	2	27	15	1.53
41729776--41729829	26	2.1	26	89	0	81	46	11	14	27	1.79
41730271--41730317	20	2.2	21	92	7	78	40	6	19	34	1.77
41733151--41733377	101	2.2	101	81	10	275	25	17	28	29	1.97
41733189--41733373	51	3.7	50	82	6	196	23	18	27	30	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41733295--41733375	26	3.2	26	65	28	73	22	14	29	33	1.94
41733380--41733469	46	2.0	44	82	8	110	25	16	24	33	1.96
41733597--41733628	16	2.0	16	93	0	55	59	0	15	25	1.36
41744704--41744765	26	2.4	26	88	0	88	19	16	27	37	1.93
41752156--41752232	26	3.0	26	81	7	93	18	10	25	45	1.81
41752166--41752235	26	2.7	26	88	0	104	18	11	28	41	1.85
41769075--41769326	35	7.2	35	84	0	315	18	14	28	38	1.91
41769069--41769326	105	2.5	105	86	0	354	18	14	28	39	1.89
41770163--41770187	13	1.9	13	100	0	50	32	0	16	52	1.44
41773019--41773124	50	2.1	50	85	3	142	28	22	31	17	1.97
41773415--41773453	20	2.0	20	90	10	62	56	5	23	15	1.59
41781918--41781951	7	4.9	7	86	13	52	88	11	0	0	0.52
41781917--41781952	8	4.9	8	80	19	51	88	11	0	0	0.50
41781917--41781952	14	2.5	14	95	4	63	88	11	0	0	0.50
41781915--41781953	15	2.6	14	88	11	60	89	10	0	0	0.48
41784537--41784593	25	2.3	25	84	6	71	29	10	3	56	1.50
41785236--41785273	6	6.3	6	87	0	58	76	2	21	0	0.91
41787362--41787391	15	1.9	16	93	6	53	6	13	3	76	1.11
41813142--41813193	18	2.8	18	77	11	52	38	9	0	51	1.35
41814091--41814130	20	2.1	20	86	9	57	65	5	10	20	1.42
41814304--41814363	26	2.3	28	72	21	67	50	10	11	28	1.71
41817971--41818129	72	2.2	72	93	0	264	17	29	25	27	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41836807--41836837	16	1.9	16	93	0	53	51	3	0	45	1.17
41838077--41838162	9	9.4	9	88	7	120	39	27	10	22	1.87
41838235--41838329	45	2.2	41	77	15	120	17	2	28	51	1.57
41838308--41838337	13	2.3	13	100	0	60	16	0	43	40	1.48
41842068--41842120	18	2.9	17	86	5	70	43	0	16	39	1.49
41848790--41848814	13	1.9	13	100	0	50	36	0	8	56	1.29
41848950--41848997	18	2.7	18	83	0	60	43	4	16	35	1.67
41851890--41851929	18	2.2	19	86	4	55	47	2	12	37	1.55
41851962--41852090	17	7.6	17	78	3	134	41	12	11	34	1.79
41852398--41852872	138	3.4	138	84	1	567	27	19	23	29	1.98

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