genome.fa.s1.2.7.7.80.10.50.1000.179.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  179  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)
53650783--53650845	29	2.2	29	85	0	81	31	26	15	25	1.96
53660653--53660811	79	2.0	79	100	0	318	32	21	11	34	1.89
53670994--53671018	5	5.0	5	100	0	50	60	0	0	40	0.97
53671329--53671355	2	13.5	2	100	0	54	51	0	0	48	1.00
53674185--53674226	20	2.1	20	86	0	57	47	0	7	45	1.30
53677540--53677725	41	4.5	41	91	0	291	30	19	25	24	1.98
53680572--53680619	21	2.3	21	96	0	87	54	16	8	20	1.68
53682085--53682126	20	2.1	20	86	0	57	47	0	7	45	1.30
53692274--53692431	9	16.7	9	67	17	54	57	5	3	34	1.36
53692275--53692339	27	2.5	26	80	9	69	61	3	3	32	1.27
53692301--53692427	19	6.6	18	73	19	71	57	5	2	34	1.35
53692823--53692847	5	5.0	5	100	0	50	60	0	0	40	0.97
53694499--53694528	6	5.2	6	96	4	53	50	0	0	50	1.00
53698567--53698641	30	2.5	30	84	2	87	34	9	8	48	1.65
53701642--53701690	24	2.0	24	84	7	64	30	16	20	32	1.94
53705477--53705518	19	2.2	20	82	4	50	30	7	11	50	1.66
53710206--53710315	33	3.3	32	78	7	94	27	22	17	32	1.96
53714034--53714062	2	15.0	2	92	7	51	48	0	0	51	1.00
53715687--53715721	8	4.1	8	92	7	52	25	2	0	71	1.00
53717908--53717951	19	2.4	17	82	14	52	56	2	6	34	1.38
53718695--53718732	2	19.0	2	100	0	76	50	0	0	50	1.00
53720429--53720499	18	3.9	18	68	23	51	46	2	4	46	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53729147--53729185	21	1.9	21	89	5	62	43	2	20	33	1.65
53732274--53732333	12	5.2	12	83	4	70	25	3	5	66	1.27
53733259--53733317	29	2.0	30	90	3	93	47	15	6	30	1.71
53734727--53734814	10	8.7	10	72	17	58	32	2	0	64	1.06
53734758--53734878	30	4.0	30	78	12	140	36	3	0	60	1.13
53734778--53734865	21	4.3	21	71	16	85	34	3	0	62	1.12
53734728--53734852	41	3.1	41	83	13	145	33	2	0	64	1.07
53734829--53734873	20	2.2	21	92	4	74	35	4	0	60	1.17
53734733--53734878	70	2.1	70	85	6	197	36	2	0	60	1.11
53738127--53738221	29	3.3	28	82	7	102	42	2	0	55	1.11
53738125--53738282	39	4.3	39	76	18	183	40	2	0	56	1.12
53738135--53738275	40	3.5	42	90	5	222	40	2	0	56	1.14
53738127--53738285	69	2.3	70	89	5	241	40	2	0	56	1.13
53738174--53738238	31	2.2	30	94	5	114	38	3	0	58	1.14
53738215--53738272	29	2.0	29	83	6	73	36	3	0	60	1.14
53738242--53738291	22	2.3	23	82	6	68	46	2	0	52	1.12
53749717--53749756	21	1.9	21	85	10	55	45	2	0	52	1.14
53753961--53754030	24	3.0	24	79	8	81	34	5	2	57	1.37
53753962--53754057	24	4.0	24	77	10	79	36	7	2	54	1.40
53754811--53754934	30	4.1	30	93	1	203	25	24	6	43	1.78
53754821--53754928	15	7.2	15	67	12	78	25	22	7	44	1.79
53759598--53759709	30	3.7	30	92	4	190	25	20	7	47	1.75
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53759598--53759705	15	7.2	15	63	12	60	25	20	7	46	1.77
53767897--53767946	25	2.0	25	100	0	100	28	20	16	36	1.93
53771267--53771322	29	1.9	29	89	7	87	39	19	17	23	1.92
53776322--53776453	21	6.3	20	81	5	122	46	18	21	12	1.82
53781206--53781248	23	2.0	23	86	9	63	48	4	6	39	1.51
53801921--53802046	47	2.7	47	78	2	137	29	13	19	38	1.90
53809355--53809385	15	2.0	16	93	6	55	58	0	0	41	0.98
53848693--53848725	17	2.0	17	88	5	50	69	0	0	30	0.88
53851111--53851286	50	3.5	50	82	3	205	31	21	23	23	1.98
53851495--53851526	12	2.7	12	95	0	55	56	6	18	18	1.62
53855180--53855238	31	1.9	31	82	6	75	37	13	6	42	1.71
53855885--53855921	17	2.1	18	90	5	58	67	0	0	32	0.91
53858933--53858961	15	1.9	15	100	0	58	20	0	0	79	0.74
53860424--53860448	13	1.9	13	100	0	50	44	0	0	56	0.99
53869696--53869732	2	18.5	2	100	0	74	48	0	0	51	1.00
53878237--53878295	26	2.3	27	79	8	68	32	11	15	40	1.83
53878992--53879054	2	32.5	2	90	6	103	49	0	1	49	1.10
53883026--53883073	15	3.3	15	76	5	53	66	2	2	29	1.14
53884806--53884830	7	3.6	7	100	0	50	24	0	0	76	0.80
53886369--53886415	25	1.9	25	86	4	69	51	4	4	40	1.41
53906066--53906128	27	2.3	27	86	0	81	42	4	11	41	1.61
53907722--53907786	29	2.3	28	77	15	71	33	6	4	55	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53912329--53912361	14	2.5	14	90	9	52	81	0	18	0	0.68
53913217--53913253	18	2.1	18	90	10	58	32	0	5	62	1.18
53916766--53916941	45	4.0	45	84	1	230	26	15	24	32	1.96
53916777--53916941	90	1.9	88	89	2	258	27	16	24	31	1.96
53920077--53920101	7	3.6	7	100	0	50	24	12	0	64	1.27
53927383--53927420	2	19.0	2	100	0	76	50	0	0	50	1.00
53928240--53928321	34	2.4	34	91	0	137	23	23	4	48	1.70
53929434--53929500	29	2.3	30	79	10	75	41	11	7	38	1.70
53931032--53931090	25	2.4	25	80	5	66	55	1	5	37	1.32
53932886--53933322	50	8.9	50	70	8	322	22	20	24	32	1.98
53932843--53933322	197	2.4	197	90	1	757	21	21	25	32	1.98
53932843--53933322	98	4.9	99	91	1	759	21	21	25	32	1.98
53934637--53934676	15	2.6	15	84	4	53	12	27	10	50	1.72
53937650--53937760	19	5.8	19	88	0	168	37	16	9	36	1.82
53948502--53948563	3	20.7	3	100	0	124	66	0	0	33	0.92
53954054--53954094	18	2.3	18	91	0	64	14	41	0	43	1.45
53954603--53954634	3	10.7	3	100	0	64	34	0	34	31	1.58
53960659--53960775	43	2.8	39	71	19	101	31	21	17	29	1.96
53960761--53960946	43	4.3	43	78	4	205	25	18	23	32	1.97
53960764--53960955	86	2.2	86	85	1	242	27	17	25	30	1.97
53962982--53963017	6	6.0	6	100	0	72	50	16	0	33	1.46
53965209--53965294	42	2.0	43	84	6	113	33	26	13	25	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53968995--53969064	30	2.4	30	81	11	83	62	2	5	28	1.32
53969472--53969496	5	5.0	5	100	0	50	60	20	0	20	1.37
53973336--53973391	29	1.9	29	85	7	78	51	3	5	39	1.42
53973640--53973664	5	5.0	5	100	0	50	80	0	0	20	0.72
53974936--53975027	34	2.7	33	88	6	130	33	0	32	33	1.58
53975086--53975206	41	3.0	41	82	0	143	18	27	17	37	1.93
53978729--53978757	14	2.0	15	93	6	51	27	27	10	34	1.89
53981036--53981080	14	3.1	14	90	6	72	66	0	0	33	0.92
53981270--53981317	12	4.1	12	89	5	71	33	0	6	60	1.22
53981255--53981317	23	2.8	24	81	11	80	34	1	4	58	1.29
53981508--53981559	19	2.7	19	85	8	70	23	3	1	71	1.13
53993732--53993804	12	5.9	12	70	19	53	24	6	0	68	1.14
53993732--53993799	18	3.7	18	82	5	75	23	7	0	69	1.14
53995805--53995846	21	2.0	21	85	0	57	26	21	38	14	1.91
53996990--53997024	18	1.9	18	88	11	54	54	34	2	8	1.46
54000089--54000147	25	2.5	24	88	5	84	35	1	1	61	1.16
54000708--54000767	29	2.1	29	83	0	75	26	31	6	35	1.82
54003849--54003895	23	2.0	23	100	0	94	27	8	38	25	1.85
54004902--54004954	23	2.2	24	93	3	90	22	7	5	64	1.41
54007077--54007104	14	2.0	14	100	0	56	50	0	0	50	1.00
54007385--54007454	31	2.3	30	82	2	77	48	7	17	27	1.72
54009135--54009177	19	2.4	17	81	11	50	23	6	0	69	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
54013782--54013925	68	2.1	68	82	5	166	50	2	4	42	1.36
54015705--54015742	18	2.1	19	85	14	53	68	0	10	21	1.19
54019622--54019655	17	1.9	18	94	5	61	29	5	0	64	1.17
54022351--54022405	24	2.3	24	83	0	65	34	23	25	16	1.95
54022956--54022984	10	2.7	11	89	10	51	34	20	0	44	1.52
54027218--54027251	17	2.1	16	88	5	50	47	5	8	38	1.59
54027557--54027677	52	2.3	52	91	4	192	27	13	30	28	1.94
54028020--54028047	14	2.0	14	100	0	56	35	7	42	14	1.73
54038945--54038993	19	2.5	19	93	3	80	16	18	4	61	1.50
54052589--54052648	31	1.9	31	86	6	86	36	13	8	41	1.74

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