genome.fa.s9.2.7.7.80.10.50.1000.178.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  178  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)
57046988--57047146	86	1.8	86	85	2	221	30	9	17	42	1.81
57050061--57050163	27	3.8	28	83	6	140	20	17	21	40	1.91
57056556--57056597	21	2.0	22	95	4	77	38	14	26	21	1.91
57056561--57056604	21	2.1	21	91	0	70	38	18	25	18	1.92
57058154--57058193	15	2.6	16	88	4	55	35	0	45	20	1.51
57058674--57058802	5	26.6	5	86	12	189	41	0	0	58	0.98
57058994--57059041	22	2.2	22	81	7	53	68	6	22	2	1.23
57059399--57059442	23	1.9	23	90	9	72	54	0	18	27	1.44
57059679--57059725	24	2.0	23	84	12	60	51	4	14	29	1.62
57066042--57066122	5	16.6	5	78	19	91	41	0	0	58	0.98
57066042--57066123	34	2.4	35	84	11	100	42	0	0	57	0.98
57066704--57066747	23	1.9	23	90	9	72	54	0	18	27	1.44
57066984--57067030	24	2.0	23	84	12	60	51	4	14	29	1.62
57072567--57072608	22	2.0	21	85	4	57	30	4	19	45	1.71
57074873--57074910	19	2.1	19	85	5	51	71	5	0	23	1.07
57075148--57076711	153	10.3	152	86	6	2048	52	7	9	30	1.62
57075393--57075444	13	4.0	13	75	9	52	65	7	1	25	1.30
57075853--57075904	13	4.0	13	75	9	52	65	7	1	25	1.30
57075139--57076711	454	3.5	453	89	3	2313	52	7	9	30	1.62
57076722--57076785	22	2.9	22	97	0	119	10	42	32	14	1.80
57076870--57076912	11	4.0	11	85	11	54	30	0	2	67	1.03
57078351--57078392	21	2.0	22	90	4	68	61	0	35	2	1.09
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57079996--57080033	18	2.0	20	90	10	62	55	13	0	31	1.38
57080861--57080892	5	6.4	5	100	0	64	18	0	0	81	0.70
57082045--57082110	27	2.4	27	85	5	89	30	18	19	31	1.96
57085682--57085712	2	15.5	2	100	0	62	51	48	0	0	1.00
57094514--57094540	13	2.1	13	100	0	54	48	7	22	22	1.75
57100043--57100158	47	2.5	46	81	8	135	42	25	13	18	1.87
57104349--57104409	27	2.3	27	97	0	113	42	11	11	34	1.77
57105085--57105110	2	13.0	2	100	0	52	50	0	0	50	1.00
57105884--57105913	14	2.1	15	93	6	53	60	6	0	33	1.23
57105787--57105961	89	1.9	91	90	4	284	56	8	6	29	1.53
57106019--57106065	18	2.6	18	82	0	58	59	4	4	31	1.36
57107719--57108352	44	14.7	44	72	14	315	27	22	20	28	1.99
57107761--57108181	128	3.3	127	75	11	485	29	22	20	27	1.99
57107717--57108271	260	2.1	261	94	1	963	28	23	20	27	1.99
57107985--57108400	217	1.9	217	89	1	645	28	21	20	29	1.98
57108651--57108741	44	2.1	44	95	0	164	31	28	16	23	1.96
57108792--57108928	43	3.1	43	69	4	139	23	27	23	25	2.00
57108747--57109010	88	3.0	88	93	1	431	23	25	24	26	2.00
57108747--57108974	44	5.2	45	68	4	167	21	25	25	28	1.99
57118247--57118284	16	2.4	16	86	4	51	65	2	10	21	1.35
57122933--57122968	2	18.0	2	100	0	72	50	0	0	50	1.00
57124970--57125025	24	2.3	24	96	0	103	66	7	8	17	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57134342--57134371	2	15.0	2	100	0	60	50	0	0	50	1.00
57135480--57135524	2	23.0	2	86	4	65	48	0	51	0	1.00
57137234--57137303	35	2.0	35	100	0	140	25	0	34	40	1.56
57139996--57140039	23	1.9	23	85	0	61	45	2	6	45	1.42
57141826--57141871	14	3.1	14	87	6	56	36	0	2	60	1.09
57147848--57148047	62	3.2	61	79	8	190	53	3	3	40	1.33
57147894--57148050	68	2.2	69	73	10	158	54	4	2	38	1.34
57149774--57149925	43	3.5	43	76	8	121	24	16	26	32	1.96
57157994--57158042	23	2.1	23	84	0	62	22	22	34	20	1.97
57158465--57158504	19	2.1	19	90	0	62	40	0	2	57	1.12
57158475--57158553	38	2.0	40	85	4	108	37	1	2	58	1.20
57161102--57161154	20	2.7	20	82	5	63	41	28	16	13	1.86
57169629--57169731	25	4.2	25	83	1	109	32	19	25	23	1.98
57171386--57171436	21	2.4	21	78	12	52	15	1	9	72	1.19
57174602--57174667	22	3.1	21	76	8	55	10	9	12	68	1.40
57176198--57176226	7	4.3	7	95	4	51	58	10	0	31	1.31
57176849--57176889	19	2.1	20	86	4	57	31	17	9	41	1.82
57178923--57179084	43	3.8	44	70	7	116	25	17	27	29	1.98
57183715--57183841	20	6.3	20	69	8	69	41	17	28	12	1.86
57197293--57197360	35	1.9	35	100	0	136	27	22	8	41	1.83
57203220--57203244	9	2.8	9	100	0	50	32	36	0	32	1.58
57206436--57206480	18	2.5	18	85	7	65	37	0	17	44	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57211579--57211612	4	8.5	4	100	0	68	26	0	0	73	0.83
57217731--57217765	18	1.9	18	88	11	54	68	8	0	22	1.16
57218621--57218651	9	3.4	9	90	0	53	25	12	22	38	1.90
57218705--57218741	9	4.1	9	92	0	65	45	13	10	29	1.77
57220490--57220515	5	5.2	5	100	0	52	19	19	19	42	1.90
57221292--57221331	13	2.7	16	81	14	50	50	0	0	50	1.00
57221292--57221356	31	2.2	30	86	10	89	46	0	0	53	1.00
57221347--57221386	13	2.9	14	88	7	55	57	0	0	42	0.98
57222868--57222900	2	16.5	2	100	0	66	48	0	0	51	1.00
57225852--57225900	9	5.4	9	80	9	64	40	20	10	28	1.85
57225852--57225905	18	2.9	18	86	2	81	40	20	11	27	1.86
57225975--57226012	20	2.0	20	89	5	60	23	0	10	65	1.23
57225939--57226023	20	4.2	19	70	16	55	27	1	8	63	1.30
57228510--57228607	28	3.5	28	90	0	151	30	11	26	31	1.91
57237504--57237547	22	2.1	21	83	8	54	59	2	0	38	1.10
57239111--57239152	14	2.9	15	85	7	59	69	9	0	21	1.17
57249649--57249702	18	2.7	21	72	19	60	29	18	11	40	1.85
57249661--57249695	18	1.9	18	100	0	70	28	17	14	40	1.88
57255975--57256002	14	2.0	14	100	0	56	50	7	21	21	1.72
57258462--57258491	15	1.9	16	93	6	53	60	0	0	40	0.97
57258450--57258493	22	2.0	21	87	12	63	61	0	0	38	0.96
57266144--57266188	19	2.3	20	82	17	60	33	2	2	62	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57272004--57272209	29	7.0	29	69	10	114	23	25	14	36	1.92
57272047--57272212	30	5.6	29	68	10	102	25	24	12	37	1.90
57272019--57272212	59	3.3	59	85	2	264	24	24	12	38	1.91
57297953--57298130	40	4.5	40	82	1	205	33	17	27	21	1.96
57297973--57298034	20	3.1	19	68	9	52	37	17	29	16	1.92
57299512--57299667	82	1.9	82	97	0	294	34	13	20	31	1.91
57319888--57319947	24	2.5	24	86	2	86	28	11	16	43	1.83
57324565--57324595	2	15.5	2	100	0	62	51	0	0	48	1.00
57328281--57328330	16	3.2	16	72	16	59	54	2	4	40	1.31
57328266--57328338	31	2.3	32	92	4	121	60	2	4	32	1.30
57328269--57328319	16	3.3	15	71	17	50	60	1	5	31	1.31
57328454--57328495	17	2.4	17	81	14	50	30	4	11	52	1.59
57329682--57329767	27	3.2	27	74	9	86	13	12	38	34	1.84
57332200--57332360	33	4.9	33	83	3	157	45	15	19	18	1.85
57332200--57332363	66	2.5	66	81	3	190	46	15	20	18	1.84
57332251--57332392	64	2.2	65	79	2	151	50	14	15	19	1.78
57353935--57354127	45	4.3	45	81	4	219	39	18	19	22	1.92
57353905--57354081	90	2.0	90	81	8	209	38	18	18	23	1.93
57353938--57354149	90	2.4	90	81	1	228	39	18	18	22	1.92
57354094--57354184	45	2.0	45	85	4	121	43	17	19	18	1.88
57353847--57354192	135	2.6	136	72	9	323	41	17	19	21	1.91
57355055--57355108	20	2.7	20	94	0	90	51	5	22	20	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57356607--57356649	13	3.5	13	75	18	56	46	16	2	34	1.60
57356605--57356651	23	2.0	23	95	0	85	44	17	2	36	1.60
57356609--57356658	23	2.2	23	88	0	73	50	14	2	34	1.54
57357619--57357643	4	6.2	4	100	0	50	28	0	0	72	0.86
57361106--57361132	5	5.4	5	100	0	54	81	0	0	18	0.69
57362031--57362096	13	5.5	13	76	20	81	48	15	0	36	1.45
57362029--57362098	23	3.0	23	97	0	131	47	15	0	37	1.46
57372657--57372788	50	2.6	50	79	0	147	26	22	27	23	2.00
57372801--57372828	13	2.2	13	100	0	56	42	28	7	21	1.79
57384453--57384482	15	1.9	16	93	6	53	56	13	16	13	1.67

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