genome.fa.s1.2.7.7.80.10.50.1000.162.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  162  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)
47852949--47853006	18	3.1	19	78	11	75	32	20	0	46	1.51
47853038--47853481	52	8.5	52	97	1	816	26	18	1	53	1.55
47853002--47853481	157	3.1	157	95	2	822	26	19	1	52	1.56
47853470--47853509	14	2.9	14	96	0	71	32	15	0	52	1.43
47853537--47853589	14	3.0	19	71	28	62	30	18	1	49	1.59
47856593--47857301	106	6.5	107	88	8	899	24	16	15	43	1.87
47857173--47857201	10	2.7	11	94	5	51	10	0	3	86	0.69
47861267--47861305	20	2.0	20	85	10	53	38	10	12	38	1.78
47861820--47861904	30	3.0	28	79	16	102	40	0	4	55	1.21
47861888--47861930	21	2.0	21	86	8	61	16	2	9	72	1.21
47863710--47863772	17	3.5	17	87	12	90	30	7	11	50	1.66
47864286--47864680	92	4.3	92	93	0	673	38	10	10	40	1.74
47866831--47866862	9	3.6	9	100	0	64	34	21	34	9	1.86
47867785--47867826	16	2.6	16	92	0	66	42	7	2	47	1.43
47868804--47868872	3	22.7	3	91	2	111	33	2	0	63	1.09
47873116--47873172	14	4.1	14	78	14	57	57	0	7	35	1.26
47875210--47875467	44	5.7	43	70	18	157	28	22	18	31	1.97
47875221--47875401	98	1.8	98	85	4	258	29	20	17	32	1.96
47875318--47875467	44	3.5	42	80	5	165	28	22	18	30	1.97
47875319--47875487	86	1.9	87	87	7	245	27	22	18	31	1.97
47875123--47875613	184	2.7	185	88	3	706	28	21	18	31	1.97
47875493--47875612	44	2.7	43	83	3	134	29	21	19	30	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47875506--47875614	44	2.5	43	84	1	137	29	21	20	29	1.98
47905556--47906034	113	4.2	113	90	4	754	24	23	26	25	2.00
47905556--47906034	224	2.1	226	92	4	790	24	23	26	25	2.00
47906285--47906315	15	2.1	15	100	0	62	19	0	48	32	1.49
47906288--47906331	15	3.1	15	84	12	58	20	0	45	34	1.51
47906575--47906607	14	2.3	15	94	5	59	33	0	27	39	1.57
47906599--47906676	21	3.7	21	71	10	61	25	0	37	37	1.56
47906631--47906663	14	2.4	14	90	10	50	24	0	42	33	1.55
47907073--47907226	85	1.8	83	84	5	211	42	14	14	27	1.85
47907255--47907292	20	1.9	20	88	0	58	71	2	0	26	1.00
47907181--47907734	141	4.1	139	86	6	721	45	11	15	27	1.80
47907505--47907734	123	1.8	125	89	6	369	45	9	14	30	1.77
47907749--47908012	133	2.0	133	91	3	435	50	12	14	22	1.77
47907848--47907915	28	2.4	30	82	12	97	55	14	10	19	1.67
47911393--47911425	17	1.9	17	100	0	66	30	6	6	57	1.47
47912195--47912374	42	4.3	42	86	5	238	25	20	21	32	1.97
47912215--47912374	85	1.9	85	92	2	268	25	21	21	30	1.99
47912215--47912376	42	3.9	41	90	4	243	25	21	21	31	1.98
47916472--47916715	19	13.5	17	68	14	80	40	9	12	36	1.77
47916518--47916648	35	3.6	35	82	8	104	38	7	12	41	1.72
47916469--47916727	37	7.2	37	75	11	209	40	9	12	37	1.76
47916469--47916727	17	14.4	17	71	14	117	40	9	12	37	1.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47917471--47917532	13	5.1	12	81	11	65	1	19	0	79	0.82
47917471--47917532	6	10.2	6	78	14	65	1	19	0	79	0.82
47917472--47917542	19	3.4	21	81	13	85	1	21	0	77	0.85
47918153--47918214	30	2.1	30	87	3	90	38	1	25	33	1.66
47918410--47918435	5	5.2	5	100	0	52	80	0	0	19	0.71
47918594--47919493	75	11.8	75	83	5	1024	34	21	17	27	1.95
47918597--47919493	148	5.9	145	81	8	904	34	20	17	27	1.95
47920390--47920422	16	2.0	17	94	5	59	6	0	9	84	0.76
47923455--47923526	36	2.0	36	100	0	144	25	27	25	22	2.00
47924627--47924686	29	2.1	29	100	0	120	16	8	6	68	1.37
47929759--47929791	18	1.9	17	88	11	50	54	0	0	45	0.99
47929930--47929983	23	2.3	23	76	17	58	51	7	3	37	1.48
47930444--47930476	16	2.0	17	88	5	50	45	9	0	45	1.35
47931109--47931145	9	4.1	9	92	0	65	45	13	10	29	1.77
47931181--47931223	21	2.0	21	82	8	52	23	34	0	41	1.55
47931333--47931377	19	2.3	21	77	14	51	24	37	0	37	1.56
47931349--47931408	30	2.0	31	86	3	86	20	36	0	43	1.52
47932681--47932721	20	2.0	20	100	0	82	46	4	14	34	1.66
47934306--47934347	13	2.9	14	80	13	50	54	0	0	45	0.99
47934310--47934346	16	2.3	16	86	13	58	59	0	0	40	0.97
47935470--47935564	31	3.1	31	93	0	154	34	31	14	18	1.92
47936953--47937003	5	10.2	5	100	0	102	39	0	21	39	1.54
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47937081--47937132	24	2.2	24	89	0	77	38	1	9	50	1.46
47937088--47937147	24	2.5	23	84	10	68	38	1	10	50	1.46
47941426--47941477	24	2.2	24	89	0	77	36	3	9	50	1.54
47941809--47941855	18	2.6	18	77	12	51	48	4	4	42	1.42
47943952--47943999	18	2.7	18	81	9	62	37	16	4	41	1.68
47945744--47945797	26	2.1	26	100	0	108	33	18	11	37	1.86
47948209--47948255	24	1.9	25	86	4	69	51	12	6	29	1.65
47948514--47948542	13	2.1	14	93	6	51	24	20	6	48	1.74
47955746--47955795	25	2.0	25	88	7	75	44	6	0	50	1.26
47955746--47955794	24	2.0	25	92	4	82	42	6	0	51	1.27
47955858--47955923	27	2.4	27	89	0	96	25	28	28	16	1.97
47956008--47956043	11	3.4	11	92	7	65	77	0	22	0	0.76
47956070--47956108	19	2.0	21	85	10	55	25	0	7	66	1.18
47956174--47956247	3	24.7	3	100	0	148	0	0	32	67	0.91
47959208--47959369	18	8.6	18	71	18	84	0	29	0	70	0.87
47959186--47959335	39	4.1	37	82	11	132	0	30	0	70	0.88
47959240--47959374	4	33.0	4	73	20	102	0	28	0	71	0.87
47959213--47959361	44	3.4	43	80	13	155	0	28	0	71	0.87
47959205--47959373	79	2.2	76	88	10	251	0	28	0	71	0.87
47959205--47959373	40	4.5	40	78	18	177	0	28	0	71	0.87
47959518--47959587	28	2.5	29	86	6	101	47	1	10	41	1.46
47967182--47967216	17	2.0	18	88	5	54	54	0	20	25	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
47968638--47968701	33	1.9	33	100	0	128	39	10	34	15	1.83
47969003--47969065	33	1.9	33	100	0	126	15	33	11	39	1.83
47977112--47977136	8	3.1	8	100	0	50	24	0	0	76	0.80
47977339--47977374	11	3.0	13	84	15	51	30	0	0	69	0.89
47977339--47977373	12	2.8	12	91	4	52	28	0	0	71	0.86
47981882--47981918	3	12.3	3	100	0	74	32	0	0	67	0.91
47983621--47983664	20	2.2	20	84	8	54	31	0	2	65	1.05
47987210--47987253	17	2.6	17	83	13	56	20	0	4	75	0.98
47987704--47987756	2	27.0	2	96	3	99	0	49	0	50	1.00
47987756--47987786	2	16.0	2	93	6	55	48	0	0	51	1.00
48000129--48000293	75	2.2	75	93	0	285	23	24	14	38	1.92
48004678--48004709	16	2.0	16	100	0	64	56	0	12	31	1.37
48005025--48005065	16	2.6	16	88	0	64	46	7	2	43	1.44
48005897--48006159	43	6.2	43	86	1	350	25	31	18	24	1.98
48005877--48006159	85	3.3	85	86	3	343	25	29	19	25	1.98
48005897--48006159	128	2.1	128	85	2	350	25	31	18	24	1.98
48012957--48013005	19	2.5	19	96	3	89	16	4	6	73	1.19
48013358--48013453	7	13.4	7	74	8	50	38	37	0	23	1.55
48013406--48013455	14	3.6	14	88	0	73	30	52	0	18	1.46
48013409--48013460	7	7.4	7	87	8	52	32	44	0	23	1.54
48013356--48013460	21	4.9	21	72	8	77	37	37	0	25	1.57
48013458--48013493	14	2.6	14	91	8	56	52	25	0	22	1.47
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
48014490--48014769	41	6.9	40	79	6	251	30	30	20	18	1.97
48014530--48014774	41	6.0	41	82	2	287	28	33	20	17	1.95
48014512--48014769	122	2.1	122	82	1	302	31	31	19	17	1.95
48015582--48015606	13	1.9	13	100	0	50	40	16	20	24	1.91
48016891--48016935	6	7.5	6	85	9	65	17	0	0	82	0.68
48017360--48017412	2	26.5	2	100	0	106	49	0	0	50	1.00
48017721--48017760	19	2.0	20	85	4	55	47	5	0	47	1.24
48022254--48023210	88	10.9	88	92	2	1428	24	23	23	28	2.00
48024861--48024901	19	2.1	19	86	13	57	9	21	0	68	1.18
48024912--48024980	14	4.9	14	78	12	70	7	1	5	85	0.79

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