genome.fa.s9.2.7.7.80.10.50.1000.93.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  93  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)
32267923--32267962	20	2.0	20	90	0	62	60	0	0	40	0.97
32268679--32268712	17	2.0	17	88	0	50	41	0	0	58	0.98
32268643--32268727	20	4.3	18	74	18	55	38	0	1	60	1.05
32269579--32269723	27	5.4	27	79	6	132	18	30	17	33	1.95
32269572--32269723	54	2.8	54	84	2	171	19	30	17	33	1.94
32273606--32273677	24	3.0	24	93	0	117	19	29	5	45	1.73
32274041--32274075	14	2.4	15	95	4	63	22	31	8	37	1.85
32282007--32282057	25	2.0	27	81	14	63	45	21	3	29	1.70
32285608--32285686	2	39.5	2	100	0	158	50	0	0	49	1.00
32286067--32286104	18	2.1	18	100	0	76	21	10	34	34	1.87
32287464--32287497	18	1.9	18	94	5	61	70	0	29	0	0.87
32288021--32288060	16	2.5	15	88	11	62	50	0	25	25	1.50
32288112--32288209	36	2.6	36	77	7	99	45	2	21	30	1.63
32288146--32288208	18	3.5	18	75	16	67	44	0	22	33	1.53
32288391--32288457	23	3.0	23	84	8	93	19	23	20	35	1.95
32288390--32288477	21	4.1	21	85	5	104	20	22	21	35	1.96
32289346--32289374	11	2.6	11	100	0	58	93	6	0	0	0.36
32293519--32293558	16	2.5	16	88	11	64	25	25	0	50	1.50
32293916--32294033	40	3.0	40	83	1	139	32	22	22	22	1.98
32294081--32294277	41	4.8	41	78	6	168	16	23	27	31	1.96
32294142--32294237	40	2.4	41	85	5	142	13	27	28	31	1.94
32294957--32295007	27	1.9	26	88	4	75	41	0	11	47	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32296326--32296377	27	1.9	27	88	7	79	44	0	11	44	1.40
32297688--32297722	18	1.9	18	88	11	54	31	14	28	25	1.95
32301521--32301569	21	2.3	21	89	0	71	36	18	42	2	1.62
32301974--32302106	42	3.1	42	88	3	196	33	21	23	21	1.97
32303127--32303166	19	2.0	20	85	4	55	20	0	10	70	1.16
32311638--32311702	34	1.9	34	93	0	112	32	18	16	32	1.94
32311726--32311819	15	6.4	15	71	4	66	26	19	23	30	1.98
32311756--32311822	28	2.4	27	80	7	80	29	20	20	28	1.98
32313259--32313530	151	1.8	147	79	10	318	26	11	4	57	1.53
32313573--32313619	21	2.2	21	80	0	58	27	6	10	55	1.58
32319499--32319954	89	5.1	88	83	3	538	30	21	23	25	1.99
32319499--32319865	177	2.1	177	93	2	639	29	19	23	27	1.98
32319499--32319932	177	2.5	177	89	2	613	30	19	23	25	1.98
32319530--32320055	89	5.9	90	83	4	289	30	21	23	25	1.99
32320077--32320389	44	7.1	44	66	11	138	30	19	24	25	1.98
32320047--32320522	132	3.6	132	90	1	758	30	18	25	25	1.98
32320508--32320672	50	3.3	49	92	1	258	34	20	17	27	1.95
32321146--32321187	19	2.2	19	87	8	59	45	2	35	16	1.61
32321173--32321218	20	2.2	21	84	7	58	60	6	19	13	1.54
32322015--32322104	23	3.9	23	75	11	85	32	6	4	56	1.45
32322041--32322165	47	2.7	46	77	14	116	36	6	2	55	1.39
32322088--32322137	24	2.1	24	85	7	66	36	6	2	56	1.36
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32322208--32322265	24	2.3	26	82	11	77	34	0	3	62	1.12
32322214--32322251	17	2.2	18	85	4	51	34	0	2	63	1.09
32322289--32322320	16	2.0	16	93	0	55	34	0	6	59	1.23
32322383--32322411	10	2.7	11	89	10	51	24	0	0	75	0.80
32324993--32325039	23	2.0	23	91	0	76	42	21	4	31	1.72
32326204--32326311	36	3.0	36	90	4	157	34	19	11	35	1.87
32326207--32326315	35	3.1	35	89	5	157	33	19	10	36	1.85
32338786--32338895	32	3.5	32	81	6	134	38	20	21	20	1.94
32338915--32338967	27	2.0	27	85	14	74	37	24	22	15	1.92
32339120--32339294	27	6.6	27	84	2	219	25	20	18	36	1.95
32339093--32339262	53	3.2	52	78	8	182	24	18	19	38	1.93
32339120--32339294	79	2.2	81	85	5	239	25	20	18	36	1.95
32341200--32341238	18	2.2	17	86	13	53	33	0	20	46	1.51
32341456--32341577	23	5.3	23	81	0	163	22	22	24	31	1.98
32341456--32341577	46	2.7	46	89	0	190	22	22	24	31	1.98
32341995--32342131	27	5.1	27	85	0	184	24	19	20	35	1.96
32341990--32342131	54	2.6	54	84	4	205	25	20	19	34	1.96
32343636--32343708	27	2.7	27	86	0	101	27	19	21	31	1.97
32346806--32346962	44	3.7	41	77	13	158	33	28	19	19	1.96
32346855--32347046	42	4.6	41	82	6	206	31	25	17	26	1.97
32350055--32350241	95	2.0	95	90	2	295	31	21	21	25	1.98
32351548--32351624	29	2.5	31	83	8	113	19	24	11	44	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32361879--32361950	29	2.4	29	86	4	92	20	29	11	38	1.87
32361783--32361950	30	5.7	29	75	7	97	22	28	13	35	1.92
32373172--32373263	48	1.9	48	97	0	175	32	0	18	48	1.48
32373193--32373228	13	2.8	13	91	4	56	33	0	16	50	1.46
32375733--32375857	50	2.5	50	82	0	151	21	28	23	26	1.99
32380695--32380762	32	2.1	32	81	10	77	60	0	2	36	1.12
32383379--32383561	66	2.8	66	81	0	215	21	27	24	26	2.00
32386899--32386939	2	20.5	2	100	0	82	48	0	0	51	1.00
32387978--32388035	29	2.0	29	100	0	116	41	20	20	17	1.90
32391490--32391523	15	2.2	16	89	5	52	32	2	0	64	1.08
32392710--32392754	2	22.0	2	88	8	65	48	2	2	46	1.26
32393287--32393501	116	1.9	116	97	0	412	55	13	12	18	1.68
32397005--32397055	16	3.2	16	85	0	66	43	5	25	25	1.77
32397232--32397344	41	2.8	39	81	10	131	47	3	2	46	1.33
32400031--32400085	26	2.1	27	80	16	71	30	0	16	52	1.44
32401227--32401265	20	2.0	20	89	0	60	33	5	20	41	1.74
32406319--32406352	5	7.0	5	93	6	61	41	0	0	58	0.98
32407306--32407418	22	5.0	22	78	10	120	17	26	18	37	1.93
32407293--32407418	47	2.7	46	87	6	175	17	26	19	37	1.93
32407293--32407372	25	3.3	24	82	10	110	15	27	22	35	1.94
32408435--32408747	159	2.0	161	88	1	477	50	15	15	19	1.77
32411845--32411870	11	2.4	11	100	0	52	19	0	15	65	1.27
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32412122--32412149	13	2.2	13	100	0	56	50	21	0	28	1.49
32412049--32412252	83	2.5	82	89	1	300	49	14	6	28	1.69
32412330--32412782	157	2.9	154	81	7	434	31	13	16	37	1.88
32413243--32413279	15	2.4	16	86	13	51	16	5	0	78	0.93
32414022--32414082	28	2.2	28	85	11	81	32	4	1	60	1.28
32425570--32425766	108	1.8	108	85	0	277	27	14	7	50	1.69
32426124--32426340	107	2.0	107	98	0	416	33	14	23	28	1.94
32426655--32427343	44	15.8	44	76	5	563	29	20	24	25	1.99
32426653--32427254	131	4.6	130	83	4	622	29	20	24	24	1.99
32426699--32427210	87	5.9	87	75	4	260	29	20	24	25	1.99
32426786--32427339	175	3.2	175	92	0	894	29	20	24	25	1.99
32428059--32428095	15	2.4	16	86	13	51	16	5	0	78	0.93
32428861--32428921	28	2.2	28	85	11	81	32	4	1	60	1.28
32429236--32429276	2	21.0	2	95	5	75	51	0	0	48	1.00
32432471--32432516	6	7.7	6	95	0	83	15	67	0	17	1.24
32432540--32432566	6	4.5	6	100	0	54	18	66	0	14	1.25
32432489--32432600	51	2.2	51	91	0	179	26	51	0	20	1.53
32434984--32435020	9	4.0	9	89	3	56	21	0	8	70	1.13
32435430--32435458	15	1.9	15	100	0	58	55	0	0	44	0.99
32441428--32441457	3	10.0	3	100	0	60	33	0	0	66	0.92
32442609--32442673	30	2.2	29	78	13	69	46	12	1	40	1.51
32448640--32448723	44	1.9	44	87	0	123	45	15	7	32	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32449085--32449128	21	2.2	20	83	4	52	63	6	4	25	1.38
32452906--32453029	59	2.1	61	90	3	198	42	6	24	26	1.78
32452906--32453029	30	4.1	30	90	3	196	42	6	24	26	1.78
32469322--32469630	153	2.0	153	89	3	474	29	22	26	21	1.99
32481125--32481268	72	2.0	72	91	0	234	27	7	18	45	1.77
32481459--32481486	14	2.0	14	100	0	56	57	0	0	42	0.99
32481437--32481489	24	2.2	25	86	10	74	52	0	1	45	1.11
32481519--32481603	32	2.6	33	79	5	102	44	17	11	25	1.83
32481596--32481635	20	2.0	20	90	0	62	50	12	10	27	1.72
32481584--32481650	34	1.9	35	90	3	109	46	13	8	31	1.74

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