genome.fa.s9.2.7.7.80.10.50.1000.116.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  116  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)
39599354--39599555	51	4.0	49	80	5	194	26	16	27	29	1.97
39604648--39604704	27	2.1	27	93	0	78	31	7	24	36	1.82
39617641--39617693	24	2.2	24	87	9	74	62	1	30	5	1.29
39617735--39617811	38	2.0	38	92	0	127	29	40	0	29	1.57
39619032--39619087	27	2.1	27	93	0	94	32	12	12	42	1.80
39627112--39627142	15	2.1	15	100	0	62	51	0	6	41	1.27
39627114--39627151	15	2.5	15	91	0	58	55	2	5	36	1.37
39627796--39627841	22	2.1	22	84	8	58	67	0	2	30	1.03
39627778--39627841	31	2.2	29	88	8	94	65	0	1	32	1.02
39638005--39638034	12	2.5	12	94	0	51	30	40	23	6	1.80
39639222--39639263	15	2.8	16	83	16	54	47	0	16	35	1.47
39644034--39644078	22	2.0	22	87	8	65	26	2	20	51	1.59
39654546--39654662	62	1.9	62	83	11	154	49	5	5	40	1.47
39654641--39654728	19	4.8	18	70	20	58	51	1	2	45	1.21
39656327--39656547	43	5.1	43	79	5	232	31	28	17	23	1.97
39656327--39656547	86	2.6	86	83	3	275	31	28	17	23	1.97
39661690--39661797	39	2.7	39	92	2	180	20	22	19	37	1.94
39662196--39662244	14	3.4	14	79	20	57	30	44	2	22	1.64
39662206--39662248	15	2.9	15	93	3	70	32	44	2	20	1.65
39662451--39662561	7	15.7	7	70	10	57	36	37	0	24	1.62
39662469--39662517	15	3.3	15	80	5	55	34	38	0	26	1.57
39662523--39662587	21	3.1	20	82	8	76	40	41	0	18	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39662092--39662675	295	2.0	291	84	7	756	42	27	2	28	1.67
39662953--39663173	41	5.4	41	81	7	225	29	29	20	19	1.97
39662953--39663173	82	2.7	83	81	4	254	29	29	20	19	1.97
39663220--39663270	25	2.0	25	88	3	75	31	23	13	31	1.93
39670961--39671011	25	2.0	25	100	0	102	45	19	7	27	1.78
39671415--39671596	50	3.7	50	81	3	181	21	26	21	30	1.99
39709939--39710013	20	3.8	20	70	0	78	34	17	20	28	1.95
39709927--39710015	40	2.2	40	83	0	106	37	14	19	29	1.91
39709806--39710021	100	2.2	99	83	3	265	37	19	18	25	1.94
39712581--39712754	27	6.5	27	75	10	119	40	18	20	21	1.92
39712568--39712736	53	3.2	52	76	9	146	40	18	19	21	1.92
39712581--39712808	27	8.5	26	77	6	111	40	19	18	21	1.92
39712677--39712841	27	6.1	27	80	4	163	38	20	16	24	1.93
39712677--39712841	53	3.1	53	83	1	195	38	20	16	24	1.93
39712901--39712960	24	2.5	24	78	5	77	18	11	26	43	1.84
39713028--39713082	27	2.1	25	87	12	76	21	27	20	30	1.98
39713129--39713337	32	6.5	32	79	7	185	17	19	23	39	1.92
39713126--39713343	96	2.3	96	81	4	269	17	20	23	38	1.93
39713360--39713418	22	2.7	22	70	19	59	18	23	15	42	1.88
39716353--39716401	14	3.5	14	85	0	71	30	20	8	40	1.81
39725714--39725764	20	2.6	21	78	12	63	11	23	5	58	1.55
39725966--39726144	50	3.6	50	79	5	168	23	29	19	27	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39726036--39726160	50	2.5	50	82	2	144	20	27	23	28	1.99
39728555--39728593	12	3.2	12	85	0	51	20	23	5	51	1.67
39728815--39728860	23	2.0	23	100	0	92	17	13	21	47	1.81
39728864--39729052	50	3.6	52	78	7	170	24	26	20	28	1.99
39736699--39736736	19	1.9	19	89	5	58	36	28	18	15	1.92
39736698--39736911	20	10.8	20	68	5	119	35	21	20	23	1.96
39736708--39736901	40	4.9	40	73	3	131	35	19	20	24	1.96
39736767--39736911	60	2.4	60	83	2	175	35	19	20	24	1.95
39738528--39738596	34	2.0	34	94	0	120	28	14	18	37	1.91
39746806--39746864	21	3.0	20	75	7	66	40	23	25	10	1.86
39746860--39746971	42	2.7	42	80	2	118	39	16	25	19	1.91
39746913--39747006	21	4.5	21	67	2	64	41	18	21	19	1.90
39746894--39747006	42	2.7	42	84	0	136	41	17	21	19	1.90
39753900--39753958	29	2.1	28	84	9	75	22	22	23	32	1.98
39754453--39754486	7	4.9	7	96	0	50	20	0	50	29	1.49
39754532--39754799	110	2.4	111	82	9	294	29	3	25	41	1.72
39755749--39755781	15	2.3	15	89	5	50	33	30	3	33	1.73
39759076--39759130	21	2.6	21	100	0	110	29	18	18	34	1.94
39759637--39760010	43	8.7	43	90	0	563	25	18	30	24	1.98
39760733--39760781	23	2.1	23	85	7	64	32	12	20	34	1.90
39760917--39760982	19	3.4	18	80	15	71	56	6	1	36	1.34
39764425--39764668	43	5.7	43	82	6	275	25	29	19	25	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39764425--39764668	128	1.9	128	84	5	332	25	29	19	25	1.98
39766793--39766871	39	2.0	39	87	0	113	36	21	11	30	1.89
39768259--39768662	202	2.0	203	98	0	783	36	8	4	50	1.55
39768976--39769017	14	2.9	14	89	6	66	33	38	0	28	1.58
39769231--39769316	21	4.0	22	73	8	70	38	37	1	23	1.63
39769289--39769319	14	2.1	15	94	5	55	38	32	0	29	1.57
39768788--39769400	310	2.0	305	89	4	928	42	27	2	28	1.67
39769679--39769837	41	3.9	40	83	3	201	28	30	19	21	1.97
39770292--39770430	70	2.0	70	94	0	242	33	12	23	30	1.91
39771777--39771801	10	2.5	10	100	0	50	32	0	8	60	1.26
39774831--39774866	18	2.0	18	88	0	54	19	8	30	41	1.81
39776653--39776690	9	4.2	9	96	0	67	10	13	23	52	1.71
39799362--39799406	21	2.1	21	84	8	56	55	11	0	33	1.35
39802736--39802772	18	2.1	18	89	0	56	37	10	5	45	1.62
39803056--39803118	21	3.0	21	88	2	90	30	3	33	33	1.74
39813947--39813985	20	2.0	20	84	0	51	43	12	15	28	1.83
39817125--39817175	21	2.6	19	79	17	52	41	11	13	33	1.81
39821524--39821568	18	2.5	18	92	0	72	20	2	31	46	1.62
39828433--39828519	25	3.5	25	78	6	95	32	20	24	22	1.98
39834217--39834253	18	2.0	19	85	15	51	5	18	0	75	0.99
39837808--39837858	7	7.0	7	82	8	57	3	27	0	68	1.07
39837794--39837866	16	4.2	16	77	19	67	5	21	0	72	1.04
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39837794--39837874	17	4.6	17	73	11	65	6	20	0	72	1.05
39837842--39837900	24	2.4	25	83	13	77	3	18	0	77	0.90
39842277--39842333	15	3.8	15	78	0	51	71	8	3	15	1.24
39848672--39848714	11	4.0	11	78	6	52	6	0	23	69	1.12
39850321--39850362	17	2.6	16	75	17	50	26	4	0	69	1.08
39850406--39850438	15	2.1	16	88	5	50	57	6	0	36	1.23
39850686--39850730	9	5.1	9	89	2	56	33	4	2	60	1.29
39851085--39851109	9	2.8	9	100	0	50	32	8	0	60	1.26
39850698--39851458	379	2.0	379	96	0	1387	37	16	17	29	1.91
39854295--39854327	13	2.5	13	95	0	57	36	18	15	30	1.91
39854382--39854461	39	2.1	39	92	0	133	33	16	17	32	1.92
39869617--39869665	25	2.0	25	87	0	71	36	12	14	36	1.83
39869625--39869679	25	2.2	26	80	9	69	40	10	12	36	1.79
39872213--39872287	20	4.0	18	71	20	64	45	1	4	49	1.29
39872726--39872782	6	9.2	6	96	3	96	15	19	0	64	1.28
39874879--39874922	23	1.9	23	85	0	61	40	4	6	47	1.50
39880235--39880290	30	1.9	28	82	13	69	60	10	14	14	1.58
39882745--39882800	30	1.9	28	82	13	69	60	10	14	14	1.58
39889217--39889286	34	2.0	34	86	5	95	17	8	7	67	1.40
39897446--39897485	13	3.2	12	92	7	62	65	2	2	30	1.19
39897480--39897504	8	3.1	8	100	0	50	60	0	0	40	0.97
39897598--39897633	14	2.7	13	91	8	63	44	0	0	55	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39899513--39899556	22	2.0	23	86	4	63	65	2	0	31	1.05
39901572--39901597	10	2.6	10	100	0	52	0	7	0	92	0.39
39907169--39908350	394	3.0	393	94	1	2039	25	21	13	38	1.90
39909003--39909179	53	3.4	53	89	6	281	25	24	13	36	1.92
39910120--39910150	4	7.8	4	92	0	53	74	3	0	22	0.96
39911242--39911273	15	2.1	15	94	0	55	0	12	25	62	1.30
39911786--39912035	133	1.9	132	81	0	302	29	21	18	31	1.97
39911664--39912041	44	8.6	44	74	2	292	29	19	19	31	1.96
39917957--39918032	30	2.6	29	79	4	82	28	23	19	27	1.98
39919964--39920065	41	2.5	40	87	6	141	27	25	19	27	1.99

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