genome.fa.s9.2.7.7.80.10.50.1000.146.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  146  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)
48338176--48338269	34	2.7	35	82	9	120	43	12	12	30	1.80
48341253--48341281	15	2.0	15	93	6	51	51	6	20	20	1.70
48346791--48346857	33	2.0	33	100	0	134	32	7	20	38	1.81
48347288--48347370	28	2.9	29	85	3	114	21	12	22	43	1.86
48347288--48347391	29	3.7	27	81	10	109	19	11	25	44	1.84
48347480--48347556	28	2.8	28	89	0	118	10	20	25	42	1.84
48347486--48347611	28	4.5	28	80	1	99	16	16	22	44	1.86
48350968--48351019	9	5.4	9	80	11	50	71	1	1	25	1.07
48350987--48351021	3	11.3	3	93	6	61	68	0	0	31	0.90
48350990--48351019	10	3.1	10	95	4	53	70	0	0	30	0.88
48354528--48354572	18	2.4	19	81	7	56	42	2	2	53	1.25
48354960--48355006	13	3.4	14	77	19	53	8	21	0	70	1.14
48356287--48356323	14	2.6	14	91	0	56	24	5	5	64	1.36
48356586--48356635	24	2.1	24	81	7	57	46	18	4	32	1.67
48358563--48358792	95	2.4	96	83	5	295	38	3	19	39	1.67
48358825--48359364	125	4.3	126	89	1	789	33	18	21	27	1.96
48363031--48363073	18	2.4	18	88	0	59	44	9	27	18	1.80
48367617--48368158	126	4.3	126	89	0	769	28	21	17	33	1.95
48368191--48368394	89	2.2	96	83	6	260	38	19	2	39	1.65
48369604--48370201	49	12.5	48	70	10	267	31	20	22	25	1.98
48370088--48370202	47	2.5	46	82	1	131	34	17	21	26	1.95
48373318--48373353	13	2.8	13	84	16	56	30	5	0	63	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48376326--48376734	126	3.3	125	88	3	608	28	16	23	31	1.96
48379906--48380060	21	7.3	21	86	5	222	25	0	28	46	1.53
48381257--48381555	21	14.1	21	77	15	303	26	0	29	44	1.54
48381255--48381557	43	7.1	43	82	11	351	26	0	29	44	1.54
48381345--48381464	36	3.1	36	79	15	150	26	0	27	45	1.54
48381362--48381399	15	2.5	15	91	0	58	28	0	26	44	1.54
48381429--48381551	22	5.2	26	78	16	94	27	0	28	43	1.55
48381506--48381552	14	3.4	14	77	16	62	27	0	27	44	1.55
48381510--48381556	15	3.4	14	77	19	53	23	0	29	46	1.52
48381586--48381614	8	3.8	8	95	4	51	51	0	0	48	1.00
48382977--48383014	20	1.9	20	84	10	51	55	7	2	34	1.43
48383283--48383349	31	2.2	31	83	0	80	37	17	16	28	1.92
48383891--48383923	7	4.7	7	100	0	66	27	0	15	57	1.38
48384866--48384914	21	2.3	21	79	6	55	32	34	28	4	1.76
48385099--48385128	15	1.9	16	93	6	53	46	0	0	53	1.00
48385099--48385128	8	3.9	8	91	8	53	46	0	0	53	1.00
48387579--48387973	126	3.3	123	83	7	476	30	23	16	29	1.96
48392432--48392556	61	2.0	61	98	0	241	20	5	15	58	1.57
48393073--48393244	52	3.2	52	76	10	143	44	11	12	31	1.77
48393183--48393255	19	3.9	18	71	7	58	36	10	13	38	1.80
48393073--48393246	17	9.8	17	72	13	95	44	10	12	31	1.77
48393073--48393253	18	10.2	17	71	10	80	43	10	12	33	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48393176--48393260	36	2.3	39	83	6	104	40	9	11	38	1.74
48393090--48393287	107	1.8	107	80	9	233	45	10	11	33	1.73
48393300--48393346	17	2.6	19	80	12	64	44	10	17	27	1.81
48393803--48393859	5	11.4	5	85	7	71	0	19	0	80	0.71
48393804--48393847	8	5.2	8	88	5	61	0	15	0	84	0.63
48393809--48393852	21	2.0	22	95	4	81	0	15	0	84	0.63
48394331--48394368	20	1.9	19	89	5	58	0	28	0	71	0.87
48394321--48394392	34	2.2	33	85	9	94	0	26	0	73	0.83
48394324--48394392	27	2.6	26	82	8	77	0	24	0	75	0.81
48394326--48394405	18	4.4	19	71	21	57	0	27	0	72	0.85
48394314--48394385	25	2.9	26	81	6	87	0	29	0	70	0.87
48394313--48394405	46	2.0	49	83	10	122	0	30	0	69	0.88
48394310--48394412	44	2.2	50	81	16	130	0	31	0	68	0.89
48394932--48395018	30	2.9	30	78	1	93	41	8	18	32	1.79
48394947--48395047	30	3.4	30	82	5	107	44	3	16	34	1.67
48395040--48395074	17	2.1	17	94	0	61	20	0	5	74	1.02
48395399--48395860	79	6.0	77	84	6	535	35	20	16	27	1.94
48395343--48395840	149	3.3	149	85	6	515	34	22	16	26	1.95
48395396--48395859	149	3.0	154	87	5	593	34	20	16	28	1.94
48396772--48396814	6	6.8	6	84	10	59	0	2	13	83	0.74
48407717--48407894	17	10.2	17	71	17	100	45	10	11	32	1.75
48407717--48407840	52	2.4	51	82	8	144	45	10	13	30	1.77
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48407717--48407879	18	9.2	18	70	15	90	44	10	12	31	1.77
48407808--48407880	38	1.9	38	91	0	119	45	9	10	34	1.72
48407717--48407907	35	5.4	34	75	11	163	46	10	11	31	1.75
48407853--48407904	17	2.9	18	83	13	72	48	11	3	36	1.58
48407937--48407982	17	2.6	19	80	16	62	41	10	15	32	1.82
48408448--48408506	20	2.7	22	85	12	77	0	18	1	79	0.81
48408456--48408506	8	6.1	8	79	6	57	0	21	0	78	0.75
48408454--48408506	24	2.2	24	87	9	74	0	20	0	79	0.74
48408836--48408862	14	1.9	14	100	0	54	3	14	0	81	0.82
48408833--48408885	22	2.4	22	81	9	54	3	16	1	77	1.01
48408833--48408895	25	2.7	23	75	20	58	3	17	1	77	0.97
48408978--48409057	25	3.1	25	82	7	81	1	31	0	67	0.99
48409010--48409053	22	2.0	21	86	4	61	0	25	0	75	0.81
48409023--48409070	25	1.9	25	83	8	62	2	27	0	70	0.98
48409643--48409736	30	3.2	29	79	11	95	44	4	17	34	1.68
48409650--48409736	29	3.0	28	79	12	88	44	3	18	33	1.66
48409728--48409763	18	2.0	18	100	0	72	22	0	5	72	1.05
48411988--48412048	3	20.3	3	96	0	113	67	1	0	31	1.01
48419504--48419560	25	2.3	23	80	16	62	31	7	3	57	1.42
48420528--48420555	14	2.0	14	100	0	56	42	0	0	57	0.99
48425175--48425225	20	2.3	23	83	9	63	74	1	1	21	1.02
48426260--48426305	22	2.1	22	88	8	67	30	0	6	63	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48429399--48429449	13	3.9	13	81	0	66	35	25	7	31	1.85
48430155--48430218	29	2.2	30	85	2	85	32	6	17	43	1.74
48452278--48452374	47	2.1	47	98	0	185	38	28	7	25	1.83
48457573--48457636	13	4.9	13	75	7	67	31	6	28	34	1.82
48457581--48457637	26	2.1	27	87	3	80	36	5	28	29	1.79
48460284--48460322	3	13.0	3	100	0	78	66	0	0	33	0.92
48461763--48462334	50	11.4	50	70	3	369	25	25	19	29	1.99
48461779--48462351	100	5.7	100	92	0	905	26	24	20	28	1.99
48462539--48462801	89	2.9	89	91	1	418	26	24	19	30	1.98
48462536--48462951	89	4.6	88	81	5	390	26	23	18	31	1.98
48462697--48462937	133	1.8	134	92	0	412	27	21	19	30	1.98
48462697--48462977	133	2.1	133	85	2	377	28	22	19	29	1.98
48462608--48463029	222	1.9	225	89	2	663	26	22	19	30	1.98
48462533--48463166	314	2.0	313	89	3	972	26	23	18	30	1.98
48462586--48463166	44	13.0	44	72	6	436	26	23	19	30	1.98
48462586--48463166	89	6.5	89	83	3	447	26	23	19	30	1.98
48469485--48469535	3	17.0	3	100	0	102	66	0	0	33	0.92
48491696--48492120	44	9.5	44	78	7	372	32	20	19	27	1.97
48492282--48492328	14	3.4	13	80	13	58	78	10	0	10	0.96
48495647--48495776	40	3.2	40	92	1	188	29	16	33	20	1.94
48495727--48496223	112	4.4	112	91	2	775	29	17	27	25	1.98
48499212--48499557	17	19.6	17	71	20	176	44	10	2	43	1.50
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48499203--48499479	57	4.9	57	89	5	388	44	9	2	43	1.49
48499322--48499557	74	3.1	73	81	9	228	43	11	1	43	1.49
48499425--48499449	13	1.9	13	100	0	50	36	0	8	56	1.29
48499448--48499590	61	2.4	57	87	8	196	41	11	2	44	1.52
48499562--48499606	13	3.5	13	87	0	72	40	6	2	51	1.41
48499753--48499975	73	3.1	73	99	0	437	50	1	7	40	1.38
48499754--48499943	38	5.2	38	65	16	139	52	1	7	37	1.40
48500152--48500439	51	5.7	50	95	1	486	46	20	0	33	1.51
48500012--48500439	76	5.6	77	94	2	713	46	20	0	33	1.51
48500012--48500439	127	3.4	128	97	1	772	46	20	0	33	1.51

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