genome.fa.s1.2.7.7.80.10.50.1000.135.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  135  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)
40761280--40761316	6	6.5	6	87	6	51	18	16	0	64	1.29
40776716--40776775	19	3.2	18	79	9	57	15	10	1	73	1.17
40776735--40776776	15	2.9	15	85	3	50	11	9	2	76	1.12
40777460--40777747	138	2.1	138	96	0	531	26	15	23	35	1.94
40779940--40779978	19	1.9	19	90	10	60	76	0	20	2	0.90
40781447--40781484	20	2.0	20	89	5	60	68	2	0	28	1.03
40782415--40782462	17	2.9	17	84	9	55	64	0	2	33	1.05
40782428--40782462	16	2.1	17	89	5	54	68	0	2	28	1.04
40782428--40782462	17	2.1	17	94	5	63	68	0	2	28	1.04
40784043--40784074	16	2.0	16	93	0	55	65	0	3	31	1.08
40784062--40784094	11	3.1	11	91	8	59	72	0	0	27	0.85
40784062--40784094	10	3.2	10	95	4	57	72	0	0	27	0.85
40784548--40784633	39	2.1	41	81	8	97	26	4	2	66	1.23
40784526--40784695	10	17.0	10	64	15	50	31	4	1	62	1.23
40784529--40784637	19	5.6	18	69	19	60	28	5	1	64	1.26
40784553--40784653	29	3.4	30	75	6	100	29	4	1	63	1.26
40784553--40784672	58	2.1	58	81	9	138	31	5	1	61	1.27
40785113--40785194	2	42.0	2	72	9	62	41	3	2	52	1.32
40786685--40786767	34	2.4	34	78	4	87	46	13	8	31	1.72
40788405--40788470	27	2.6	25	75	17	71	19	19	21	39	1.93
40788631--40788691	25	2.3	26	81	13	72	18	22	22	36	1.95
40790890--40790952	28	2.2	28	97	0	117	33	11	6	49	1.64
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40791152--40791205	3	18.0	3	100	0	108	33	0	0	66	0.92
40791757--40791782	13	2.0	13	100	0	52	46	0	0	53	1.00
40791769--40791815	19	2.4	19	82	3	58	42	0	2	55	1.12
40791978--40792031	20	2.7	21	78	16	60	46	1	0	51	1.11
40792561--40792615	23	2.4	23	85	11	69	25	1	10	61	1.39
40797237--40797287	21	2.5	21	90	9	79	54	11	11	21	1.68
40801088--40801151	23	2.8	22	74	6	65	42	0	0	57	0.98
40801361--40801394	11	2.9	11	91	8	50	50	0	2	47	1.16
40802117--40802160	23	1.9	24	86	9	65	68	2	0	29	1.02
40802409--40802519	58	1.9	58	83	9	145	21	15	13	49	1.78
40802909--40803054	59	2.5	59	76	7	154	51	15	14	19	1.76
40803007--40803076	31	2.3	31	97	0	131	48	12	14	24	1.78
40805168--40805192	2	12.5	2	100	0	50	52	0	0	48	1.00
40808957--40809017	5	12.2	5	75	0	50	40	19	4	34	1.73
40808945--40809017	10	7.3	10	80	0	74	41	19	5	34	1.74
40808945--40809015	30	2.4	30	80	0	88	40	19	5	33	1.75
40812566--40812622	28	2.0	28	96	0	105	40	17	10	31	1.84
40813148--40813194	19	2.6	17	78	18	51	70	0	8	21	1.14
40814217--40814266	21	2.4	21	93	0	82	8	22	0	70	1.13
40822046--40822129	8	10.5	8	76	13	84	73	0	1	25	0.90
40822046--40822130	9	9.4	9	78	16	88	74	0	1	24	0.89
40822012--40822140	47	2.8	46	88	8	194	70	0	2	27	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40822128--40822158	9	3.3	9	95	4	53	51	0	9	38	1.35
40822012--40822171	46	3.6	44	83	12	186	68	0	3	28	1.05
40824153--40824190	19	1.9	20	84	10	51	28	15	2	52	1.56
40828340--40828432	27	3.5	27	83	1	116	48	9	19	22	1.78
40831504--40831584	27	3.0	27	79	0	90	34	14	23	27	1.94
40831715--40831840	27	4.7	27	77	0	117	39	7	26	25	1.83
40831731--40831835	54	1.9	54	82	0	129	40	8	25	25	1.84
40836976--40837009	7	4.7	7	88	3	50	82	0	11	5	0.83
40837338--40837630	98	2.9	99	77	12	330	26	16	9	47	1.77
40837347--40837498	49	3.1	49	65	17	125	28	14	7	49	1.71
40838525--40838663	46	3.0	46	91	0	215	28	15	25	30	1.95
40838648--40838679	16	2.0	16	93	0	55	34	18	34	12	1.89
40838607--40838723	62	1.9	62	91	3	191	30	15	26	27	1.96
40838664--40840070	46	30.6	46	89	0	2112	27	15	25	31	1.96
40838560--40838771	108	2.0	108	92	3	356	29	14	26	29	1.95
40842266--40842295	2	15.0	2	92	0	51	46	0	3	50	1.18
40843986--40844179	51	3.8	51	80	2	246	25	15	27	30	1.96
40843984--40844171	102	1.8	102	94	0	331	25	15	27	30	1.96
40847213--40847252	18	2.2	18	86	4	53	57	20	2	20	1.52
40847958--40848020	25	2.6	25	89	2	92	14	39	22	23	1.91
40851584--40851653	36	1.9	36	85	8	97	41	1	1	55	1.17
40851753--40851812	22	2.8	21	79	18	61	71	3	1	23	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40852547--40852901	114	3.1	113	85	1	478	34	16	21	27	1.95
40859088--40859131	21	2.1	21	100	0	88	38	9	13	38	1.77
40859087--40859142	21	2.8	19	87	10	85	37	8	16	37	1.80
40859121--40859165	23	2.0	23	86	4	65	40	2	17	40	1.62
40859131--40859175	23	2.0	23	82	4	56	35	2	15	46	1.58
40859338--40859376	19	2.0	21	85	10	55	15	10	5	69	1.34
40859582--40859637	15	3.6	15	75	13	51	28	1	1	67	1.10
40859584--40859637	24	2.2	24	83	6	65	27	1	1	68	1.10
40866040--40866072	16	2.0	16	94	5	57	81	0	0	18	0.68
40866296--40866615	44	7.3	44	61	8	112	26	30	22	20	1.98
40866203--40866678	264	1.8	264	90	0	765	27	28	23	20	1.99
40866203--40866678	88	5.4	88	88	0	684	27	28	23	20	1.99
40866692--40867067	44	8.7	44	82	6	446	27	17	25	29	1.98
40866693--40867074	126	2.9	129	87	5	511	28	17	25	29	1.97
40866692--40867029	170	2.0	170	88	4	504	28	16	25	29	1.97
40867909--40867983	19	3.8	19	91	6	123	37	9	16	37	1.80
40867910--40867972	21	3.1	21	95	4	112	38	9	14	38	1.78
40868180--40868218	19	2.0	21	85	10	55	15	10	5	69	1.34
40868440--40868479	3	13.3	3	84	10	55	32	0	0	67	0.91
40868424--40868478	15	3.7	15	74	16	53	30	0	1	67	1.01
40868426--40868477	12	4.1	12	80	14	52	28	0	1	69	0.99
40877076--40877106	15	2.1	15	93	0	53	22	0	9	67	1.19
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40877328--40877396	22	3.1	22	93	0	111	26	26	17	30	1.97
40877709--40877737	15	1.9	15	100	0	58	37	0	6	55	1.27
40879276--40879347	30	2.5	28	80	8	81	40	8	1	50	1.41
40881984--40882169	37	5.0	37	94	0	300	37	13	20	27	1.91
40882132--40882255	46	2.8	46	91	3	200	33	16	22	27	1.96
40884399--40884446	17	2.8	17	93	0	78	43	6	2	47	1.40
40888919--40888961	20	2.2	20	83	4	61	34	2	2	60	1.22
40889528--40889585	20	2.9	19	77	10	62	37	1	0	60	1.07
40901956--40902567	132	4.6	132	90	1	811	29	26	16	27	1.97
40901956--40902803	44	19.3	44	75	6	709	29	26	16	27	1.97
40914225--40914631	107	3.8	107	93	0	665	31	18	19	30	1.96
40915398--40915428	15	2.1	15	93	0	53	58	0	9	32	1.31
40918360--40918391	16	2.0	16	100	0	64	31	18	12	37	1.88
40918904--40918942	17	2.3	17	86	0	51	15	2	7	74	1.15
40920970--40921076	56	1.9	55	90	1	169	41	10	9	39	1.71
40923246--40923354	56	2.0	55	92	5	184	40	12	8	38	1.74
40924956--40925136	100	1.8	100	80	4	222	33	13	17	35	1.89
40937539--40937577	18	2.2	17	86	13	53	33	0	20	46	1.51
40937576--40937609	17	2.0	17	100	0	68	35	5	29	29	1.81
40937699--40937727	8	3.6	8	100	0	58	24	13	27	34	1.93
40937814--40937866	23	2.3	23	93	0	97	20	20	26	32	1.98
40951474--40951629	45	3.5	45	87	1	215	43	14	20	21	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40961356--40961422	27	2.3	30	85	7	95	17	4	7	70	1.28
40963693--40963812	44	2.8	42	78	10	118	25	15	29	30	1.95
40966388--40966417	12	2.5	12	94	0	51	46	26	13	13	1.80
40982767--40982806	20	2.0	20	85	0	53	27	0	25	47	1.52
40983812--40983858	24	2.0	24	95	0	85	34	17	23	25	1.96
40989170--40989216	6	7.8	6	92	0	67	4	12	0	82	0.80
40992113--40992166	3	18.0	3	100	0	108	0	33	0	66	0.92
40992268--40992296	3	9.7	3	100	0	58	0	31	0	68	0.89
40995561--40995626	3	22.0	3	87	0	96	33	3	1	62	1.20
40995672--40995728	10	6.3	9	82	15	57	43	0	0	56	0.99

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