genome.fa.s9.2.7.7.80.10.50.1000.147.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  147  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)
48505962--48506032	21	3.4	21	84	0	88	30	16	47	4	1.66
48506356--48506478	42	2.9	42	85	0	156	27	19	22	30	1.98
48506931--48506981	17	2.7	19	79	17	61	39	19	15	25	1.91
48507283--48507356	29	2.5	29	82	4	85	24	13	13	48	1.78
48509849--48509956	39	2.7	40	74	17	107	33	4	3	58	1.36
48510349--48510379	15	2.1	15	93	0	53	25	0	12	61	1.32
48522280--48523337	44	24.7	41	70	16	368	29	19	22	28	1.98
48522285--48522654	125	2.9	127	82	7	419	29	17	23	29	1.97
48522269--48523342	342	3.1	343	92	0	1774	29	19	22	28	1.98
48522711--48522996	126	2.3	127	88	1	423	30	19	20	29	1.97
48522627--48522996	126	2.9	128	83	6	401	30	18	22	28	1.98
48523059--48523337	128	2.2	128	91	0	450	29	21	21	27	1.99
48522838--48523301	217	2.2	215	84	4	580	30	19	21	28	1.98
48525483--48525513	15	2.1	15	93	0	53	25	0	12	61	1.32
48529312--48529367	23	2.6	21	83	13	69	58	1	0	39	1.08
48532538--48532580	22	2.0	22	85	0	59	11	13	27	46	1.78
48532657--48533085	42	10.2	42	88	4	584	31	21	21	25	1.98
48532669--48533085	82	5.0	82	87	5	581	32	21	20	25	1.98
48533505--48533544	12	3.3	12	92	0	53	2	37	17	42	1.63
48533529--48533593	21	3.1	20	86	4	85	3	44	18	33	1.65
48539257--48539398	9	16.0	9	85	5	191	34	0	20	45	1.52
48539375--48539478	39	2.5	40	87	9	140	42	0	12	44	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48539458--48539501	23	1.9	23	95	0	79	38	0	18	43	1.50
48539370--48539486	39	2.9	39	78	6	108	43	0	12	42	1.48
48539500--48539656	63	2.5	63	97	0	296	42	8	7	42	1.62
48539608--48539819	27	7.6	27	70	19	141	44	9	5	40	1.60
48539545--48539819	90	3.2	87	90	6	413	44	9	6	40	1.61
48539703--48539819	27	4.4	27	83	10	150	45	10	5	39	1.60
48539707--48539819	53	2.1	54	90	8	178	44	9	5	40	1.60
48539831--48539882	13	4.0	13	77	5	52	44	1	9	44	1.48
48541986--48542027	19	2.2	19	86	0	57	19	2	50	28	1.60
48542529--48542757	74	3.1	74	66	13	209	37	23	13	24	1.92
48542468--48542847	147	2.6	147	96	0	697	37	24	12	25	1.91
48543594--48543652	23	2.5	24	74	20	61	38	33	1	25	1.66
48543942--48544118	73	2.4	74	78	8	175	29	24	19	26	1.99
48553112--48553150	19	2.1	19	100	0	78	56	5	15	23	1.59
48554841--48554916	32	2.4	32	84	2	91	39	5	3	51	1.43
48558231--48558314	36	2.2	36	83	12	96	10	13	5	70	1.33
48558268--48558331	30	2.1	30	85	0	83	9	4	6	79	1.04
48566310--48566356	23	2.0	23	83	4	58	36	6	19	38	1.77
48566885--48566928	23	1.9	23	85	0	61	36	9	9	45	1.68
48571060--48571164	24	4.4	23	70	20	81	29	4	2	62	1.30
48581969--48581994	12	2.2	12	100	0	52	15	15	23	46	1.83
48582101--48582592	113	4.3	114	82	4	553	31	18	21	28	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48582127--48582581	230	2.0	226	85	2	606	31	19	20	28	1.97
48582991--48583076	14	6.1	14	72	8	68	23	0	27	48	1.51
48582991--48583045	27	2.0	27	82	6	67	18	0	32	49	1.48
48582994--48583068	21	3.6	21	73	8	55	22	0	28	49	1.50
48583232--48583261	15	2.0	15	93	0	51	63	3	0	33	1.11
48583474--48583511	20	1.9	20	100	0	76	31	0	7	60	1.25
48584168--48584212	17	2.5	19	82	10	58	26	44	0	28	1.55
48585452--48585503	27	2.0	26	81	11	61	36	1	7	53	1.41
48585584--48585663	9	8.6	9	77	8	79	47	16	1	35	1.55
48585561--48585686	48	2.6	48	96	0	225	45	14	3	37	1.61
48585579--48585667	18	5.3	18	76	21	104	46	14	1	38	1.52
48585697--48585736	19	2.2	19	86	8	57	42	2	20	35	1.65
48587020--48587048	14	2.1	14	93	6	51	34	0	10	55	1.34
48587763--48587995	43	5.4	43	66	10	116	34	21	19	24	1.97
48587764--48587995	86	2.7	86	79	2	243	34	21	19	24	1.97
48588494--48588559	32	2.1	32	85	5	89	46	0	0	53	1.00
48590170--48590251	28	3.0	28	76	3	94	29	17	14	39	1.89
48591454--48591479	6	4.3	6	100	0	52	34	0	0	65	0.93
48614625--48614651	12	2.2	12	100	0	54	29	29	11	29	1.91
48625867--48625949	28	3.0	28	76	0	85	30	18	13	38	1.88
48627763--48627797	4	8.8	4	100	0	70	48	25	0	25	1.51
48629132--48629167	18	1.9	18	94	5	63	38	0	0	61	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48630746--48630808	31	2.1	30	85	8	83	47	1	0	50	1.10
48643172--48643204	15	2.1	16	88	5	50	57	0	3	39	1.14
48645742--48645787	14	3.2	14	84	12	58	52	8	8	30	1.62
48650712--48650769	22	2.6	22	81	7	64	41	17	5	36	1.72
48657430--48657459	15	2.0	15	100	0	60	26	26	13	33	1.93
48657751--48657790	21	1.9	21	84	0	53	42	0	5	52	1.23
48657749--48657796	21	2.3	21	74	0	51	45	0	4	50	1.21
48680597--48680630	18	1.9	18	88	5	52	70	2	5	20	1.21
48683655--48683750	23	4.0	23	68	16	70	55	6	0	38	1.25
48687836--48687870	3	11.7	3	100	0	70	68	0	0	31	0.90
48693837--48693875	17	2.3	17	86	0	51	0	12	10	76	1.01
48693854--48693922	22	3.2	21	74	8	59	2	13	8	75	1.15
48694928--48694968	17	2.3	18	87	8	57	78	2	19	0	0.87
48695529--48695594	27	2.4	27	73	12	64	6	28	3	62	1.34
48699985--48700021	19	1.9	19	94	0	65	35	8	8	48	1.62
48703380--48703419	21	2.0	21	85	14	57	47	0	32	20	1.50
48707399--48707426	4	7.0	4	100	0	56	25	25	25	25	2.00
48708319--48708394	12	6.5	11	72	11	53	60	0	2	36	1.11
48708800--48708908	3	36.3	3	77	14	100	64	0	5	30	1.16
48708800--48708908	48	2.3	49	84	12	138	64	0	5	30	1.16
48708798--48708910	39	2.8	40	83	12	126	64	0	5	30	1.15
48710399--48711134	375	2.0	375	92	2	1246	25	19	19	34	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48711043--48711184	50	2.8	50	87	8	209	25	19	23	31	1.98
48710399--48711051	125	5.2	125	98	0	1243	25	19	19	35	1.95
48710858--48711447	300	2.0	300	97	0	1108	26	19	20	33	1.96
48710983--48711309	175	1.9	175	82	5	410	25	19	20	34	1.96
48711156--48711434	125	2.2	125	80	3	339	26	20	20	32	1.97
48711326--48711447	50	2.4	49	80	8	147	26	19	19	34	1.96
48713641--48713704	24	2.6	25	80	7	78	7	1	9	81	0.94
48713811--48714329	273	1.9	273	92	0	876	31	20	19	29	1.97
48715995--48716043	19	2.5	20	80	6	57	42	10	18	28	1.83
48717428--48717723	108	2.7	108	91	2	466	34	21	16	27	1.95
48718024--48718099	12	6.5	11	72	11	53	60	0	2	36	1.11
48718507--48718612	3	35.3	3	76	14	94	64	0	5	30	1.17
48718504--48718614	39	2.8	39	80	16	113	63	0	5	30	1.16
48720025--48720210	49	3.8	49	77	7	180	36	16	20	26	1.93
48730015--48730071	28	2.0	28	100	0	114	31	28	15	24	1.96
48731620--48731690	10	7.3	10	75	10	58	54	0	5	39	1.24
48738821--48738874	25	2.2	25	93	6	92	59	11	16	12	1.61
48740424--48740478	22	2.5	22	77	11	58	43	3	3	49	1.37
48755132--48755175	18	2.5	17	82	10	52	27	0	6	65	1.17
48761331--48761376	22	2.0	23	91	8	76	50	4	2	43	1.34
48770169--48770193	13	1.9	13	100	0	50	24	16	16	44	1.86
48772606--48772659	22	2.3	24	84	6	67	7	7	9	75	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48772604--48772659	23	2.4	23	85	8	69	7	7	8	76	1.15
48773135--48773197	29	2.3	27	82	15	76	69	1	3	25	1.12
48773315--48773384	18	3.8	18	80	14	72	58	0	2	38	1.13
48773395--48773419	11	2.3	11	100	0	50	56	0	0	44	0.99
48773546--48773602	20	2.9	19	75	10	60	59	5	3	31	1.36
48773595--48773635	16	2.3	19	84	16	61	70	2	0	26	0.99
48773992--48774044	10	5.4	10	80	8	56	32	1	1	64	1.15
48778644--48778987	44	7.8	44	71	12	240	28	24	18	28	1.98
48778607--48779009	132	3.1	132	94	0	698	28	24	19	28	1.98
48778618--48779003	88	4.4	87	71	12	304	28	24	18	27	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