genome.fa.s9.2.7.7.80.10.50.1000.164.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  164  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)
52306570--52306608	2	19.5	2	100	0	78	51	0	0	48	1.00
52307454--52307569	43	2.7	43	71	14	121	31	29	15	23	1.95
52309043--52309095	23	2.4	21	78	6	52	66	3	3	26	1.26
52309058--52309091	17	1.9	17	88	5	50	61	2	5	29	1.34
52313236--52313268	9	3.7	9	91	0	57	36	30	3	30	1.73
52314058--52314087	14	2.1	14	93	0	51	43	10	6	40	1.64
52314175--52314230	7	7.7	7	76	21	53	30	0	1	67	1.01
52314175--52314229	15	3.8	14	77	17	58	29	0	1	69	0.99
52314723--52314760	18	2.1	19	90	5	60	81	5	2	10	0.94
52318254--52318286	2	16.5	2	93	0	57	48	0	3	48	1.17
52321326--52321409	42	2.0	42	97	0	159	30	10	15	42	1.81
52321804--52321848	2	22.5	2	100	0	90	48	0	0	51	1.00
52322422--52322489	33	2.1	33	83	10	86	51	2	0	45	1.16
52326238--52326315	34	2.2	34	95	4	138	21	20	28	29	1.98
52327961--52328019	29	2.0	29	100	0	118	45	20	6	27	1.76
52328834--52328895	23	2.8	23	81	11	60	59	4	8	27	1.46
52338504--52338541	18	2.1	18	85	9	51	36	5	0	57	1.21
52348870--52348953	40	2.1	40	86	4	116	25	16	19	39	1.92
52349066--52349201	40	3.4	40	80	7	141	26	16	23	33	1.95
52350740--52350796	9	6.3	9	78	8	53	57	1	8	31	1.39
52350728--52350801	27	2.6	30	83	10	84	56	2	6	33	1.40
52351627--52351660	8	4.1	8	92	3	50	11	2	2	82	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
52354855--52354888	17	1.9	17	88	5	50	61	2	8	26	1.40
52366273--52366383	43	2.6	43	84	2	107	30	31	18	19	1.96
52371060--52371261	7	28.6	7	71	10	54	41	33	1	23	1.63
52371064--52371182	14	8.4	15	74	10	81	37	41	0	21	1.53
52371076--52371122	21	2.2	22	85	11	62	42	42	0	14	1.46
52371053--52371140	28	3.1	28	80	4	88	45	36	0	18	1.49
52371163--52371246	14	5.9	14	73	5	62	42	28	3	25	1.71
52371186--52371261	21	3.6	21	70	10	64	47	23	3	25	1.69
52371281--52371323	14	3.1	14	75	0	50	46	34	0	18	1.50
52371571--52371822	113	2.2	112	90	0	387	30	25	18	25	1.98
52373081--52373132	17	3.1	17	77	5	52	25	5	3	65	1.32
52373087--52373128	16	2.6	16	78	14	50	26	4	4	64	1.33
52374073--52374233	80	2.0	80	98	0	313	14	26	16	42	1.86
52382591--52382657	30	2.2	30	94	2	116	20	7	10	61	1.53
52384904--52384935	9	3.4	10	87	12	50	56	0	0	43	0.99
52384891--52384940	18	2.6	19	76	17	59	60	0	0	40	0.97
52387076--52387119	3	14.7	3	100	0	88	34	0	0	65	0.93
52387224--52387269	23	2.0	23	83	8	58	36	0	13	50	1.41
52388049--52388102	3	18.0	3	100	0	108	33	0	0	66	0.92
52390703--52390735	12	2.8	12	90	4	50	60	6	12	21	1.53
52397689--52397718	15	2.1	14	93	6	51	50	0	0	50	1.00
52399044--52399156	57	2.0	58	82	8	142	14	0	35	49	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
52399040--52399155	29	4.0	28	72	8	99	13	0	34	50	1.48
52403287--52403329	22	2.0	22	100	0	86	32	4	13	48	1.63
52414947--52414981	3	11.7	3	87	0	52	60	0	2	37	1.12
52414946--52414981	15	2.4	15	95	0	63	58	0	2	38	1.13
52415977--52416009	3	11.0	3	100	0	66	33	0	33	33	1.58
52416383--52416435	26	2.0	28	85	7	74	20	20	13	45	1.84
52418952--52418979	5	5.6	5	100	0	56	82	17	0	0	0.68
52421737--52421922	86	2.2	86	86	1	266	29	26	18	25	1.98
52421737--52421922	43	4.3	43	80	6	225	29	26	18	25	1.98
52423472--52423705	7	32.9	7	72	13	111	43	34	0	21	1.59
52424013--52424378	113	3.3	115	80	7	416	28	21	20	28	1.98
52425621--52425653	3	11.0	3	100	0	66	33	0	0	66	0.92
52432756--52432832	30	2.6	30	76	0	82	41	31	19	7	1.80
52441195--52441245	2	25.5	2	100	0	102	49	0	0	50	1.00
52441720--52441772	26	2.0	28	85	7	74	20	20	13	45	1.84
52443963--52444055	15	6.3	15	69	13	59	17	1	31	50	1.53
52446020--52446057	2	19.0	2	94	0	67	50	2	0	47	1.15
52448741--52448919	50	3.6	49	75	7	137	24	26	20	28	1.99
52448804--52448926	49	2.5	50	82	2	149	22	27	22	26	1.99
52450223--52450266	18	2.4	18	88	7	63	20	9	18	52	1.72
52452416--52452541	43	2.9	43	82	8	148	31	28	17	22	1.96
52462265--52462310	16	2.9	16	78	15	51	26	6	4	63	1.38
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
52469929--52470025	33	2.8	35	72	20	89	45	3	1	50	1.24
52470202--52470267	13	5.1	13	84	0	87	39	25	4	30	1.76
52470403--52470588	82	2.2	82	78	11	175	41	16	14	27	1.87
52475195--52475272	38	2.1	38	95	0	138	25	17	17	38	1.92
52476381--52476554	51	3.5	50	80	14	200	43	18	17	20	1.89
52476396--52476563	45	3.6	45	82	11	194	42	20	17	20	1.90
52476483--52476508	6	4.3	6	100	0	52	50	15	15	19	1.79
52479022--52479067	19	2.4	20	82	7	60	50	4	0	45	1.21
52479041--52479100	18	3.6	16	74	19	52	53	1	0	45	1.10
52480640--52480684	22	2.0	22	100	0	90	46	17	8	26	1.78
52483671--52483882	107	2.0	107	91	0	343	33	17	18	29	1.95
52490787--52490880	40	2.3	40	85	7	129	25	14	22	37	1.93
52492030--52492066	19	2.0	18	89	5	56	62	2	2	32	1.23
52493139--52493229	43	2.1	43	87	2	130	34	10	10	43	1.75
52493630--52493737	42	2.5	43	88	4	157	21	19	25	34	1.96
52496103--52496136	17	1.9	17	88	5	50	61	2	8	26	1.40
52501315--52501344	15	2.0	15	100	0	60	40	6	13	40	1.71
52502298--52502357	18	3.5	17	69	15	52	28	6	1	63	1.29
52504429--52504675	132	1.9	132	84	3	336	27	21	18	32	1.97
52504654--52505164	89	5.8	89	91	0	772	29	24	15	31	1.95
52504654--52505195	44	12.2	44	80	2	582	29	24	15	30	1.95
52509318--52509357	19	2.0	20	85	4	55	47	10	20	22	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
52518000--52518029	15	2.0	15	100	0	60	40	6	13	40	1.71
52518455--52518515	23	2.6	22	77	10	59	54	1	24	19	1.54
52518982--52519039	17	3.5	17	74	21	61	25	5	5	63	1.36
52520423--52520466	24	1.9	24	90	9	74	36	0	2	61	1.09
52520563--52520590	9	3.1	9	100	0	56	57	10	0	32	1.33
52520533--52520742	68	3.1	68	94	1	370	45	8	5	40	1.57
52520631--52520658	9	3.1	9	100	0	56	57	10	0	32	1.33
52520731--52520772	16	2.6	16	92	0	66	42	7	2	47	1.43
52520746--52520801	23	2.5	23	82	2	69	44	1	1	51	1.22
52526291--52526350	30	2.0	30	90	0	93	6	18	30	45	1.75
52548037--52548069	17	1.9	17	88	11	50	21	0	12	66	1.23
52548187--52548280	2	46.5	2	71	12	50	38	3	5	53	1.40
52552471--52552523	26	2.0	28	92	7	92	16	22	11	49	1.78
52554707--52554733	2	13.5	2	100	0	54	51	0	0	48	1.00
52561769--52561797	14	2.1	14	100	0	58	37	13	20	27	1.91
52564912--52564952	21	1.9	22	85	5	57	48	2	12	36	1.54
52569280--52569321	16	2.5	17	81	11	52	61	0	0	38	0.96
52575897--52575922	13	2.0	13	100	0	52	30	0	38	30	1.58
52577375--52577408	16	2.1	16	88	0	50	50	11	23	14	1.76
52578946--52578978	16	2.0	17	88	5	50	24	3	12	60	1.46
52583551--52583601	19	2.6	20	78	6	59	37	1	5	54	1.36
52585645--52585694	20	2.5	20	86	0	73	18	22	18	42	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
52586450--52586479	2	15.5	2	93	6	53	46	0	0	53	1.00
52587240--52587274	17	2.1	17	94	0	61	25	20	25	28	1.99
52591664--52591699	18	2.0	18	88	0	54	55	2	0	41	1.14
52604516--52604593	32	2.4	32	85	6	95	20	25	37	16	1.93
52605998--52606161	40	4.1	40	89	0	247	11	15	28	43	1.82
52606834--52606872	12	3.2	12	88	0	60	5	17	43	33	1.72
52610131--52610191	32	1.9	32	83	6	79	45	1	3	49	1.28
52615477--52615515	2	19.5	2	100	0	78	48	0	0	51	1.00
52626221--52626286	32	2.1	32	97	0	123	21	12	22	43	1.85
52627937--52627993	26	2.1	27	81	15	66	47	0	5	47	1.24

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