genome.fa.s9.2.7.7.80.10.50.1000.12.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  12  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)
5618821--5618862	19	2.3	19	87	4	59	59	0	7	33	1.25
5623773--5623799	3	9.0	3	100	0	54	33	33	0	33	1.58
5631231--5631288	21	2.7	21	84	10	73	10	3	18	67	1.35
5633526--5633552	2	13.5	2	100	0	54	48	0	0	51	1.00
5650234--5650278	18	2.5	18	100	0	90	0	57	0	42	0.98
5651402--5651467	34	1.9	35	84	3	89	42	12	10	34	1.77
5656863--5656894	5	6.6	5	96	3	57	84	0	15	0	0.63
5661570--5661709	31	4.5	31	77	12	153	24	17	12	45	1.83
5671495--5671533	17	2.3	17	100	0	78	15	48	0	35	1.45
5682990--5683026	16	2.3	16	95	0	65	40	5	32	21	1.76
5683259--5683293	18	2.0	17	88	5	52	54	0	2	42	1.15
5683239--5683307	28	2.6	27	72	21	63	52	1	1	44	1.19
5683276--5683434	47	3.5	46	73	18	143	46	3	3	47	1.34
5686337--5686371	14	2.5	14	90	0	52	25	0	0	74	0.82
5692675--5692813	69	2.0	69	97	0	260	28	15	15	39	1.89
5697613--5697919	154	2.0	154	99	0	605	41	22	14	21	1.90
5703050--5703108	29	2.0	29	100	0	118	32	23	10	33	1.88
5703637--5703667	16	1.9	16	93	0	53	67	6	6	19	1.35
5703998--5704053	2	28.0	2	92	0	94	51	0	46	1	1.11
5714955--5714999	23	2.0	23	86	4	65	37	6	17	37	1.76
5714942--5715002	19	2.9	21	81	11	72	36	6	18	39	1.76
5715532--5715607	36	2.1	36	80	11	84	38	9	1	51	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5715924--5715967	3	14.7	3	100	0	88	31	0	0	68	0.90
5717464--5717507	18	2.5	17	77	3	52	47	0	0	52	1.00
5732689--5732820	40	3.4	38	76	7	113	25	18	26	30	1.98
5733005--5733033	14	2.0	15	93	6	51	27	3	20	48	1.66
5752935--5752990	23	2.4	23	78	3	67	39	1	0	58	1.08
5753783--5753829	20	2.3	20	78	10	51	6	17	42	34	1.74
5754063--5754100	18	2.1	18	90	0	58	42	10	26	21	1.85
5754154--5754221	30	2.3	30	84	0	82	4	17	48	29	1.67
5755783--5755841	11	5.4	11	69	15	50	45	0	32	22	1.52
5755787--5755845	23	2.7	21	90	10	100	47	0	28	23	1.52
5755787--5755843	10	5.3	10	76	15	60	47	0	29	22	1.52
5768761--5768787	14	1.9	14	100	0	54	51	33	0	14	1.43
5773922--5773976	27	2.1	27	86	10	78	40	1	3	54	1.28
5780144--5780191	25	1.9	25	87	8	71	37	22	8	31	1.84
5789184--5789222	2	19.5	2	100	0	78	48	0	0	51	1.00
5789251--5789308	24	2.5	24	75	8	66	68	5	8	17	1.33
5795528--5795835	168	1.8	169	87	5	464	20	25	4	50	1.66
5795961--5796003	11	3.8	11	80	17	52	65	2	2	30	1.18
5811047--5811110	30	2.1	30	100	0	128	12	18	14	54	1.70
5813899--5813948	26	1.9	26	91	0	82	34	10	26	30	1.89
5828470--5828531	19	3.0	20	81	18	65	33	0	3	62	1.11
5835543--5835710	71	2.4	71	93	0	300	27	18	16	38	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5843027--5843068	19	2.2	19	83	8	50	33	0	2	64	1.07
5850368--5850401	17	1.9	18	88	5	52	35	26	0	38	1.57
5852963--5853163	51	3.9	51	98	1	377	31	17	23	27	1.97
5852963--5853290	102	3.1	103	81	14	397	31	16	23	28	1.96
5853143--5853184	21	2.0	21	100	0	84	23	23	19	33	1.97
5853164--5853280	44	2.7	44	93	2	200	29	16	23	30	1.96
5866012--5866055	22	2.0	22	90	0	70	47	6	6	38	1.57
5868779--5868809	3	10.3	3	92	0	53	32	38	0	29	1.57
5869779--5869803	2	12.5	2	100	0	50	52	0	0	48	1.00
5873323--5873957	318	2.0	317	98	0	1225	41	16	14	27	1.88
5886912--5886936	2	12.5	2	100	0	50	48	0	0	52	1.00
5889110--5889151	21	2.0	21	95	0	75	35	9	26	28	1.88
5897313--5897478	87	1.9	87	98	0	323	32	5	30	31	1.80
5944715--5944752	20	1.9	20	88	0	58	28	5	13	52	1.61
5948365--5948406	20	2.1	20	86	0	57	47	0	7	45	1.30
5953323--5953364	20	2.1	20	86	0	57	47	0	7	45	1.30
5956356--5956646	50	5.8	50	88	0	411	21	30	21	26	1.99
5956973--5957029	30	1.9	30	88	0	87	31	21	5	42	1.75
5958010--5958216	80	2.7	78	77	8	201	35	3	16	43	1.66
5960352--5960381	2	15.0	2	100	0	60	50	0	0	50	1.00
5961527--5961556	11	2.7	11	89	0	51	16	0	23	60	1.36
5965564--5965649	22	3.9	22	90	0	118	29	27	15	27	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
5972967--5973029	31	2.0	31	93	0	108	36	1	7	53	1.40
5972973--5973048	31	2.6	29	84	12	84	34	2	10	52	1.50
5973999--5974033	3	12.0	3	93	6	63	65	0	0	34	0.93
5976666--5976703	3	12.7	3	100	0	76	34	0	0	65	0.93
5988443--5988481	19	2.1	19	100	0	78	15	15	20	48	1.81
5992115--5992359	124	2.0	124	97	0	463	44	16	11	26	1.82
6006838--6006889	19	2.7	19	75	21	54	55	1	0	42	1.10
6014035--6014076	3	13.7	3	90	5	66	33	0	0	66	0.92
6017554--6017612	27	2.2	28	81	6	68	40	5	6	47	1.52
6023696--6023731	17	2.1	18	89	5	56	58	5	5	30	1.44
6027032--6027099	26	2.7	25	77	6	66	33	22	26	17	1.96
6027052--6027107	26	2.2	26	80	6	60	33	23	28	14	1.94
6037565--6037618	21	2.5	22	84	6	65	57	1	3	37	1.27
6037592--6037674	39	2.1	39	93	0	139	65	0	1	33	1.01
6037601--6037669	11	6.6	11	76	20	69	60	0	1	37	1.06
6039266--6039299	2	17.0	2	100	0	68	50	0	0	50	1.00
6056363--6056428	20	3.3	20	81	8	73	53	4	1	40	1.31
6056357--6056421	19	3.4	19	78	6	69	56	4	1	36	1.29
6056374--6056446	27	2.7	26	82	14	78	53	2	1	42	1.23
6071324--6071492	84	2.0	84	92	0	284	52	8	14	24	1.69
6071595--6071642	21	2.3	21	85	3	71	39	2	27	31	1.68
6073571--6073742	86	2.0	85	84	10	226	47	6	5	40	1.53
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6073731--6073770	17	2.4	17	87	8	55	45	7	15	32	1.74
6073788--6073844	16	3.6	16	90	0	87	45	3	3	47	1.37
6073818--6073879	22	2.7	23	90	5	90	48	1	1	48	1.21
6075507--6075568	29	2.1	29	82	5	72	33	12	24	29	1.92
6081057--6081199	36	3.9	36	94	1	232	44	9	18	27	1.79
6083818--6083948	57	2.4	54	83	10	158	35	18	13	32	1.90
6084380--6084420	21	1.9	22	85	5	57	46	9	9	34	1.70
6085850--6085889	2	20.0	2	100	0	80	50	0	0	50	1.00
6118177--6118300	34	3.5	35	86	8	164	35	17	19	27	1.94
6118177--6118320	36	4.0	36	86	8	197	36	15	21	27	1.93
6118284--6118406	46	2.8	44	87	7	178	33	17	22	26	1.96
6119738--6119833	31	3.1	31	92	3	165	31	10	13	44	1.77
6124353--6124392	13	3.0	13	82	7	53	42	12	2	42	1.56
6136567--6136603	20	1.9	20	94	5	67	43	2	8	45	1.47
6142086--6142166	39	2.1	38	97	2	153	28	13	19	38	1.90
6158512--6158554	13	3.2	13	80	12	52	60	6	0	32	1.23
6167400--6167458	22	2.7	22	91	0	91	35	15	25	23	1.94
6178837--6178862	2	13.0	2	100	0	52	50	0	0	50	1.00
6180285--6180364	22	3.6	22	86	0	115	30	26	13	30	1.94
6181650--6181694	7	6.6	7	97	2	83	57	0	0	42	0.98
6181633--6181688	21	2.6	21	88	5	76	62	0	0	37	0.95
6181991--6182018	14	2.0	14	100	0	56	7	28	0	64	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
6181971--6182015	19	2.5	18	83	16	58	6	26	0	66	1.16
6183703--6183727	12	2.1	12	100	0	50	28	32	8	32	1.86
6185010--6185051	18	2.4	18	84	4	50	42	0	2	54	1.13
6185568--6185613	19	2.4	20	85	7	60	67	4	0	28	1.10
6186051--6186076	2	13.0	2	100	0	52	50	0	0	50	1.00
6187796--6187825	14	2.1	14	100	0	60	13	20	0	66	1.24
6193166--6193269	43	2.4	43	96	0	190	31	11	22	34	1.90
6193223--6193303	37	2.2	37	93	2	137	28	12	23	35	1.91
6193218--6193438	87	2.5	87	88	1	336	28	14	23	33	1.94
6193310--6193393	36	2.3	37	87	2	116	23	13	28	34	1.92

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