genome.fa.s1.2.7.7.80.10.50.1000.136.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  136  of  187  ( 22383 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)
40995696--40995728	2	16.5	2	100	0	66	48	0	0	51	1.00
40997988--40998040	24	2.2	24	89	0	88	56	16	15	11	1.67
40997990--40998027	18	2.1	18	90	0	58	55	18	10	15	1.68
41000125--41000166	18	2.3	18	87	0	57	76	4	2	16	1.07
41001086--41001177	47	2.0	46	95	2	166	42	20	23	13	1.87
41002582--41003030	45	10.0	45	75	9	317	28	21	24	25	1.99
41002582--41003297	89	8.0	90	83	4	376	27	22	24	24	2.00
41002834--41003149	44	7.1	43	65	14	149	27	27	24	20	1.99
41002713--41003302	89	6.6	89	86	1	770	28	24	24	22	1.99
41003159--41003297	45	3.1	45	66	13	106	30	20	25	23	1.99
41003302--41003459	51	3.2	50	75	10	164	27	17	26	28	1.97
41003302--41003482	97	1.9	97	88	4	276	28	17	25	28	1.97
41003302--41003535	97	2.4	97	83	6	271	29	17	24	28	1.97
41009011--41009056	22	2.1	22	96	4	85	45	0	4	50	1.21
41020836--41020876	16	2.6	16	78	21	50	31	4	0	63	1.15
41021200--41021239	20	2.0	20	85	9	55	62	2	0	35	1.09
41025085--41025123	12	3.6	12	74	25	50	79	0	0	20	0.73
41025085--41025136	20	2.6	20	100	0	104	78	0	0	21	0.74
41025094--41025144	14	3.6	14	84	7	59	80	0	0	19	0.71
41030571--41030659	28	3.2	28	91	1	144	32	23	21	22	1.98
41030991--41031060	27	2.6	26	82	8	70	27	14	17	41	1.87
41030995--41031111	54	2.2	54	80	6	130	21	13	22	42	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41031023--41031111	27	3.3	27	87	0	124	20	13	23	42	1.87
41034759--41035140	194	2.0	194	92	1	631	32	14	19	33	1.92
41044976--41045006	16	1.9	16	93	0	53	48	3	0	48	1.17
41047971--41048004	15	2.3	15	89	0	50	32	0	0	67	0.91
41047980--41048033	26	2.0	27	85	10	74	29	1	0	68	1.00
41047992--41048040	25	2.0	25	84	8	64	30	2	0	67	1.02
41047992--41048040	26	1.9	25	87	4	71	30	2	0	67	1.02
41072672--41072702	12	2.6	12	94	0	53	25	38	25	9	1.86
41079184--41079222	18	2.1	18	85	4	51	64	2	5	28	1.28
41080281--41080327	23	2.0	24	91	4	78	46	4	14	34	1.64
41084497--41084590	47	2.0	47	93	0	161	34	8	14	42	1.77
41084942--41085019	20	3.9	20	73	6	59	14	25	16	43	1.85
41087416--41087476	23	2.5	24	77	15	63	50	1	1	45	1.21
41090174--41090207	9	3.8	9	92	0	59	38	29	8	23	1.85
41095892--41095944	25	2.1	25	89	0	79	11	7	26	54	1.62
41096963--41096994	14	2.2	15	94	5	57	31	3	15	50	1.60
41099717--41099766	21	2.4	21	96	0	91	66	4	30	0	1.10
41115132--41115163	9	3.6	9	100	0	64	43	0	0	56	0.99
41115122--41115165	18	2.5	17	82	10	61	40	0	2	56	1.11
41121748--41121936	94	2.0	94	98	0	369	22	26	18	32	1.97
41121967--41121992	6	4.3	6	100	0	52	0	30	15	53	1.42
41124490--41124523	17	1.9	17	88	5	50	55	0	0	44	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41126793--41126838	23	2.0	23	100	0	92	47	8	0	43	1.34
41126795--41126844	23	2.2	23	92	0	82	52	10	0	38	1.35
41127902--41127969	20	3.3	20	67	25	61	20	27	2	48	1.64
41127887--41127969	41	2.0	41	100	0	166	25	24	2	48	1.63
41127955--41128037	40	2.1	40	100	0	166	22	34	4	37	1.76
41132748--41132807	29	2.1	28	84	6	77	28	10	15	46	1.77
41132971--41133075	52	2.0	52	96	0	192	22	9	30	37	1.86
41133078--41133358	126	2.2	124	89	5	424	30	14	21	33	1.94
41134331--41134383	17	3.0	17	71	10	52	60	0	0	39	0.97
41134331--41134393	30	2.1	30	83	13	78	60	1	0	38	1.07
41134338--41134395	30	2.0	28	87	9	82	58	1	0	39	1.08
41134426--41134531	52	2.1	51	85	1	140	33	1	31	33	1.69
41134484--41134552	22	3.1	22	87	0	102	39	1	27	31	1.66
41135776--41135846	28	2.5	28	79	4	81	28	4	18	49	1.66
41137962--41138066	53	2.0	53	96	0	192	25	34	10	29	1.89
41142236--41142274	18	2.1	19	85	4	53	33	2	7	56	1.41
41148981--41149029	20	2.5	20	89	0	71	24	22	0	53	1.47
41148987--41149019	15	2.1	16	88	5	50	21	27	0	51	1.48
41151164--41151206	21	2.1	20	87	12	61	44	6	0	48	1.29
41151172--41151309	68	2.0	70	84	9	185	50	4	2	42	1.37
41157197--41157236	20	2.0	20	95	0	71	30	22	15	32	1.94
41165460--41165631	88	2.0	88	86	0	245	29	17	27	26	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41165485--41165631	44	3.3	44	80	3	188	31	15	27	24	1.96
41171384--41171413	15	2.0	15	100	0	60	40	6	6	46	1.56
41177999--41178061	30	2.1	30	93	0	108	25	3	14	57	1.52
41190565--41190618	27	2.0	26	86	10	74	66	5	18	9	1.39
41192010--41192036	14	1.9	14	100	0	54	37	3	7	51	1.48
41192202--41192235	2	17.0	2	100	0	68	50	0	0	50	1.00
41195451--41195540	37	2.4	37	80	5	101	14	11	38	35	1.82
41198962--41199939	487	2.0	487	99	0	1938	21	15	19	44	1.87
41210192--41210244	26	2.0	26	89	7	81	26	32	18	22	1.97
41214653--41214686	16	2.1	16	100	0	68	32	11	11	44	1.77
41216337--41216424	35	2.5	35	83	0	113	42	31	9	17	1.80
41218943--41218980	15	2.5	15	95	0	67	36	5	23	34	1.78
41222266--41222320	27	2.2	23	84	12	65	14	9	0	76	1.02
41222288--41222320	6	5.7	6	85	7	50	15	3	0	81	0.80
41222284--41222320	12	3.2	12	88	3	58	16	5	0	78	0.93
41223591--41223792	72	2.8	71	82	9	234	28	24	24	22	1.99
41223729--41224006	113	2.4	114	79	6	278	26	24	24	24	2.00
41224356--41224385	15	2.0	15	93	0	51	20	0	43	36	1.52
41224361--41224410	15	3.3	15	83	8	57	16	0	46	38	1.47
41224334--41224396	22	2.8	22	80	4	72	20	1	46	31	1.61
41227144--41227216	33	2.3	31	86	6	94	19	19	23	38	1.93
41228360--41228564	25	8.0	25	92	2	320	44	20	0	34	1.52
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41228452--41228527	18	4.5	17	68	26	54	42	21	0	36	1.53
41228527--41228600	18	3.9	18	78	19	80	45	18	0	35	1.50
41228513--41228592	36	2.2	38	82	13	105	45	18	0	36	1.50
41228360--41228562	102	2.0	102	93	3	347	44	20	0	34	1.52
41228527--41228609	37	2.3	36	87	2	112	44	19	0	36	1.51
41229642--41229708	21	3.2	21	86	0	89	29	19	49	1	1.57
41230019--41230137	43	2.8	43	89	2	177	37	21	18	22	1.94
41230971--41231125	75	2.0	76	90	7	244	32	12	20	34	1.91
41233415--41233556	41	3.5	41	90	0	223	19	17	28	33	1.95
41233919--41233965	14	3.3	15	82	8	62	27	0	31	40	1.57
41233952--41233992	21	2.0	20	85	4	55	19	0	41	39	1.52
41233984--41234039	7	7.9	7	80	4	67	19	1	48	30	1.59
41233981--41234028	22	2.2	22	92	0	78	14	2	50	33	1.55
41234445--41234489	19	2.4	18	82	7	54	75	2	4	17	1.07
41234450--41234490	19	2.2	19	86	0	55	78	2	2	17	0.98
41234797--41235252	124	3.7	122	85	0	554	33	17	23	25	1.97
41234797--41235250	245	1.8	246	85	2	642	32	18	23	25	1.97
41235556--41235623	22	3.1	21	71	12	66	25	25	10	39	1.87
41236964--41237004	19	2.2	19	86	8	57	41	2	0	56	1.13
41237041--41237489	9	51.8	9	70	18	294	44	20	1	32	1.60
41237060--41237500	25	18.2	24	75	14	169	45	20	1	32	1.60
41237060--41237529	34	14.5	33	69	21	239	45	20	1	32	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41237047--41237485	16	27.9	16	69	21	204	45	20	1	32	1.59
41237351--41237485	41	3.2	41	85	6	157	44	21	2	31	1.64
41239516--41239554	18	2.2	18	86	4	53	43	5	7	43	1.55
41240986--41241025	11	3.6	11	93	6	64	22	35	0	42	1.54
41240987--41241086	51	2.0	51	86	4	139	25	27	1	47	1.59
41240986--41241073	11	7.4	11	74	15	50	23	28	1	46	1.60
41243056--41243098	13	3.5	13	75	18	56	48	18	0	32	1.48
41243054--41243100	23	2.0	23	95	0	85	46	19	0	34	1.50
41243811--41243857	19	2.4	20	82	13	62	53	10	0	36	1.36
41243869--41243931	21	3.3	19	77	16	58	66	3	1	28	1.16

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