genome.fa.s9.2.7.7.80.10.50.1000.179.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  179  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)
57393911--57393947	15	2.6	14	87	8	56	2	24	0	72	0.97
57396631--57396913	143	2.0	139	85	8	374	23	17	12	46	1.81
57404375--57404414	16	2.5	16	95	0	71	60	2	0	37	1.11
57404672--57404841	52	3.1	56	80	8	190	41	11	14	32	1.81
57405419--57405549	60	2.2	59	81	10	133	58	8	0	32	1.33
57405673--57405732	11	5.7	11	78	21	51	0	31	0	68	0.90
57405682--57405732	14	3.7	14	78	17	54	0	31	0	68	0.90
57405681--57405735	11	5.4	10	79	16	60	0	30	0	69	0.89
57405801--57405849	20	2.5	20	90	6	73	34	16	38	10	1.82
57406604--57406768	43	3.8	43	82	6	208	23	28	18	29	1.98
57407117--57407161	21	2.1	21	87	0	63	6	48	11	33	1.65
57408819--57409116	44	6.8	44	94	1	537	32	1	15	50	1.55
57409220--57409721	44	11.3	44	93	3	864	31	2	15	50	1.57
57409220--57409721	269	1.9	262	95	2	914	31	2	15	50	1.57
57409701--57409748	20	2.7	17	84	12	53	27	0	20	52	1.47
57409733--57409905	9	19.1	9	66	19	67	32	2	17	46	1.61
57409702--57409875	25	7.2	25	72	17	104	30	2	19	47	1.62
57409722--57409805	41	2.0	41	83	0	105	33	2	20	44	1.64
57409789--57409869	37	2.2	36	80	10	94	29	2	18	49	1.61
57410858--57411175	146	2.2	147	84	2	406	38	21	12	26	1.90
57410840--57411309	147	3.2	147	77	5	443	37	21	13	26	1.91
57412471--57413063	72	8.2	72	89	2	769	24	22	19	33	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57412471--57413063	145	4.1	144	85	2	764	24	22	19	33	1.97
57413879--57413953	20	3.7	19	89	8	105	32	0	5	62	1.17
57414030--57414057	9	3.1	9	100	0	56	25	10	10	53	1.67
57419311--57419344	16	2.1	16	100	0	68	47	5	5	41	1.52
57419508--57419532	7	3.6	7	100	0	50	36	0	0	64	0.94
57420437--57420493	25	2.3	25	93	0	96	22	5	7	64	1.38
57428853--57428895	20	2.3	18	88	8	59	69	4	0	25	1.07
57433586--57433810	50	4.5	50	83	1	247	21	28	21	28	1.99
57433741--57433879	69	2.0	69	95	0	251	23	31	17	26	1.97
57433809--57433938	50	2.6	50	96	0	233	22	30	20	26	1.98
57433711--57433929	119	1.8	119	95	0	393	21	31	20	26	1.98
57435743--57435779	19	1.9	19	94	0	65	32	29	8	29	1.86
57436322--57436382	30	2.0	32	90	6	99	31	1	45	21	1.61
57436328--57436390	30	2.1	30	85	8	83	33	1	44	20	1.61
57439052--57439132	29	2.8	29	96	0	144	44	17	8	29	1.78
57439193--57439232	9	4.4	9	93	0	62	40	25	10	25	1.86
57447791--57447858	30	2.2	31	84	2	84	26	19	7	47	1.75
57450030--57450139	35	3.1	35	84	2	141	13	19	29	38	1.90
57450038--57450154	35	3.4	34	78	7	110	12	17	29	41	1.86
57457837--57457887	26	2.0	26	96	0	93	37	7	15	39	1.77
57458149--57458197	21	2.3	21	89	0	71	22	32	26	18	1.97
57469247--57469300	28	2.0	28	88	3	83	44	3	7	44	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57475091--57475258	51	3.3	50	77	5	167	27	14	26	31	1.95
57475087--57475235	50	2.9	51	79	5	158	28	15	25	30	1.96
57483615--57483668	23	2.4	23	78	12	58	64	5	0	29	1.16
57501144--57501332	51	3.8	49	77	6	182	24	16	26	31	1.97
57501150--57501334	101	1.8	102	87	3	275	24	17	26	31	1.97
57501150--57501342	102	1.9	101	86	3	271	24	17	26	30	1.97
57501560--57501591	16	2.0	16	93	0	55	59	0	15	25	1.36
57504307--57504406	47	2.1	47	81	3	112	26	15	28	31	1.95
57507174--57507358	101	1.8	102	88	3	284	24	17	27	31	1.97
57507171--57507366	51	3.9	49	78	4	196	23	17	28	30	1.97
57507174--57507366	102	1.9	101	87	3	280	24	17	27	30	1.97
57507511--57507542	16	2.0	16	93	0	55	59	0	15	25	1.36
57513449--57513558	42	2.6	42	81	2	114	27	16	30	25	1.96
57519511--57519823	156	2.0	157	94	0	556	42	11	19	25	1.86
57520593--57521566	490	2.0	490	96	0	1813	30	18	20	30	1.97
57529433--57529478	20	2.2	21	96	3	85	10	19	6	63	1.48
57529445--57529488	20	2.2	20	84	8	54	9	27	4	59	1.48
57530455--57530517	29	2.2	29	94	0	108	26	20	9	42	1.83
57546571--57546624	23	2.3	23	83	3	72	57	3	7	31	1.44
57546868--57546960	23	4.0	23	77	6	98	59	4	4	32	1.37
57547800--57547844	22	2.0	22	86	4	63	33	17	6	42	1.76
57547823--57547878	19	2.9	19	97	0	103	30	19	10	39	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57548313--57548352	21	1.9	21	89	0	62	25	37	5	32	1.77
57548258--57548394	72	1.9	72	83	0	175	28	26	13	31	1.94
57548602--57548843	46	5.2	46	82	4	286	28	26	17	27	1.98
57548602--57548866	92	2.8	95	81	5	329	29	26	17	26	1.98
57551185--57551221	16	2.2	17	90	4	58	2	16	0	81	0.81
57551185--57551251	21	3.2	21	85	8	75	10	16	0	73	1.10
57551185--57551244	11	5.5	11	75	16	54	8	18	0	73	1.08
57553808--57553842	16	2.2	16	89	0	52	42	22	17	17	1.88
57555317--57555370	23	2.3	23	83	3	72	57	3	7	31	1.44
57556295--57556334	20	2.1	19	86	9	55	60	17	17	5	1.54
57556521--57556573	18	2.8	19	91	5	90	32	18	11	37	1.87
57560756--57560802	2	23.5	2	100	0	94	48	0	0	51	1.00
57573191--57573266	38	2.0	38	81	0	89	18	25	27	28	1.98
57573228--57573407	50	3.5	50	88	8	256	21	29	21	27	1.99
57575101--57575183	34	2.5	34	86	2	105	39	4	15	39	1.69
57576596--57576681	43	2.0	43	100	0	172	32	20	4	41	1.73
57576697--57576778	41	2.0	41	97	0	155	28	12	7	52	1.65
57587894--57587931	3	13.3	3	83	10	53	68	0	31	0	0.90
57587894--57587930	14	2.6	14	91	0	65	67	0	32	0	0.91
57587902--57587939	17	2.2	17	86	9	51	71	2	26	0	1.00
57587877--57587943	31	2.2	30	80	15	75	71	1	26	0	0.94
57588098--57588164	22	3.2	22	85	10	95	28	1	10	59	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57588079--57588265	101	1.9	101	91	2	313	29	1	13	56	1.44
57588237--57588358	49	2.5	49	87	0	181	32	1	13	52	1.50
57588237--57588358	27	4.9	27	73	16	120	32	1	13	52	1.50
57588279--57588336	22	2.9	19	73	14	53	36	3	10	50	1.54
57588096--57588281	19	9.2	19	73	20	128	30	1	13	55	1.45
57588492--57588558	27	2.4	27	92	2	116	37	0	8	53	1.32
57591500--57591552	21	2.6	21	85	8	65	1	22	1	73	1.03
57591502--57591552	19	2.6	19	84	9	59	1	23	1	72	1.05
57591631--57591692	27	2.3	27	77	0	70	29	32	22	16	1.95
57592973--57593020	21	2.2	22	81	3	62	47	2	2	47	1.25
57597837--57597910	13	5.7	13	77	0	76	37	25	9	27	1.87
57597837--57597910	26	2.8	26	83	0	85	37	25	9	27	1.87
57600447--57600622	63	2.8	63	80	3	210	25	25	19	29	1.99
57601126--57601166	21	2.0	21	90	0	64	73	7	19	0	1.07
57603231--57603288	30	1.9	30	82	0	71	25	24	25	24	2.00
57603312--57603371	30	2.0	30	83	3	77	43	18	11	26	1.84
57605069--57605145	14	5.0	15	71	20	52	42	14	9	33	1.77
57605085--57605124	20	2.0	20	90	0	62	50	12	10	27	1.72
57605073--57605139	34	1.9	35	90	3	109	46	13	8	31	1.74
57606058--57606115	28	2.1	28	96	0	107	44	0	15	39	1.47
57606378--57606491	49	2.3	49	78	11	119	36	17	21	23	1.94
57610127--57610153	13	2.1	13	100	0	54	0	14	22	62	1.31
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57613882--57613912	5	6.0	5	92	7	53	77	0	0	22	0.77
57618366--57618390	5	5.0	5	100	0	50	80	0	0	20	0.72
57620164--57620314	76	2.0	76	81	2	178	30	20	20	28	1.98
57620164--57620314	38	4.0	38	82	1	160	30	20	20	28	1.98
57629147--57629219	30	2.5	29	82	14	96	58	1	0	39	1.06
57629146--57629216	24	2.9	24	84	12	83	60	1	0	38	1.06
57631843--57631919	37	2.1	37	92	0	127	42	10	5	41	1.61
57632482--57632524	18	2.4	18	84	0	50	60	0	4	34	1.17
57645452--57645606	30	5.2	30	85	4	197	20	25	20	34	1.96
57645452--57645606	60	2.6	60	90	4	233	20	25	20	34	1.96

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