genome.fa.s1.2.7.7.80.10.50.1000.69.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  69  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)
20341011--20341064	23	2.2	25	78	18	69	31	18	27	22	1.97
20341017--20341064	23	2.1	23	88	7	71	31	16	29	22	1.96
20341057--20341125	26	2.7	26	81	4	95	37	21	23	17	1.94
20341151--20341208	26	2.2	26	87	0	80	17	22	24	36	1.95
20343148--20343184	18	2.1	18	100	0	74	40	27	10	21	1.86
20348514--20348655	27	5.3	27	89	0	203	41	26	15	16	1.88
20348971--20349050	28	2.9	28	92	0	142	21	21	26	31	1.98
20359999--20360031	16	2.1	16	88	5	50	18	3	3	75	1.06
20364096--20364143	25	1.9	25	91	0	78	35	8	18	37	1.81
20364683--20364726	22	2.0	22	82	8	54	27	4	6	61	1.41
20366197--20366262	25	2.7	26	79	6	75	46	0	0	53	1.00
20366199--20366261	23	2.8	22	78	19	67	47	0	0	52	1.00
20369591--20369624	16	2.1	17	88	5	52	55	0	0	44	0.99
20371542--20371655	41	2.8	41	89	1	165	25	28	21	25	1.99
20375606--20375650	17	2.6	18	82	7	56	68	0	2	28	1.01
20376805--20376833	15	1.9	15	100	0	58	20	24	20	34	1.97
20382917--20382981	24	2.7	24	73	15	71	24	23	18	33	1.96
20382916--20383021	25	4.3	24	68	13	72	23	24	18	33	1.97
20385836--20385869	16	2.1	17	94	5	61	61	20	5	11	1.50
20394221--20394267	21	2.2	21	81	7	60	27	0	4	68	1.08
20402146--20402228	3	27.7	3	85	0	112	34	0	4	60	1.18
20403913--20403954	22	1.9	22	85	0	57	47	11	14	26	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20416760--20416801	17	2.4	18	84	11	52	14	4	2	78	1.01
20421940--20421989	13	3.2	16	75	18	61	52	0	0	48	1.00
20422898--20422955	29	2.0	29	89	0	89	55	10	5	29	1.55
20423092--20423168	28	2.9	25	78	16	75	48	2	0	49	1.15
20428937--20429033	51	1.9	51	95	0	176	34	21	13	30	1.92
20432437--20432496	31	2.0	29	87	6	84	31	13	11	43	1.80
20432721--20432759	16	2.5	16	88	12	55	46	0	10	43	1.37
20433368--20433407	18	2.3	17	86	4	53	77	2	0	20	0.88
20443510--20443535	2	13.0	2	100	0	52	50	0	0	50	1.00
20447348--20447397	23	2.2	22	82	10	57	46	2	10	42	1.49
20447424--20447480	19	2.9	19	70	12	53	38	8	12	40	1.74
20447591--20447632	21	2.0	21	95	0	75	42	21	9	26	1.83
20450560--20450617	19	2.9	19	75	14	64	39	10	12	37	1.77
20453534--20453580	23	2.0	23	91	0	76	42	4	10	42	1.59
20453681--20453737	27	2.2	25	81	12	62	68	3	28	0	1.06
20454594--20454675	25	3.3	25	91	0	119	21	26	17	34	1.95
20462212--20462303	41	2.2	41	98	0	175	19	28	22	29	1.98
20463077--20463103	2	13.5	2	100	0	54	51	0	0	48	1.00
20464111--20464135	13	1.9	13	100	0	50	40	24	4	32	1.73
20464456--20464555	41	2.5	41	88	1	139	38	13	25	24	1.91
20480315--20480359	17	2.5	18	82	7	56	64	2	6	26	1.30
20482161--20482235	25	3.0	25	80	9	82	72	4	21	2	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20482191--20482238	19	2.5	20	83	16	66	75	0	25	0	0.81
20482158--20482235	31	2.4	32	78	6	86	71	3	21	2	1.14
20482197--20482238	15	2.9	15	83	16	61	76	0	23	0	0.79
20482457--20482481	12	2.1	12	100	0	50	56	0	8	36	1.29
20483895--20483925	2	15.5	2	100	0	62	48	0	0	51	1.00
20487390--20487428	5	7.8	5	88	0	60	43	0	56	0	0.99
20490996--20491065	34	2.1	34	100	0	140	47	11	27	14	1.78
20505546--20505580	17	1.9	19	88	11	56	51	0	17	31	1.45
20505672--20505735	28	2.4	28	82	15	89	34	6	18	40	1.76
20506375--20506465	35	2.6	35	87	5	121	35	16	23	25	1.95
20509273--20509368	41	2.5	37	76	18	113	42	2	16	38	1.60
20509736--20509992	136	1.9	136	89	0	397	30	21	19	27	1.98
20510773--20510830	20	3.0	20	92	7	95	55	0	0	44	0.99
20532764--20532788	12	2.1	12	100	0	50	24	36	24	16	1.94
20532948--20533042	9	10.4	9	85	6	120	40	26	10	23	1.87
20536770--20536804	14	2.6	14	95	4	63	54	5	0	40	1.24
20544090--20544124	7	4.9	7	86	6	52	85	0	0	14	0.59
20547697--20547759	33	1.9	32	87	3	90	46	33	9	11	1.72
20548911--20549011	32	3.2	33	78	14	97	30	1	4	62	1.27
20548954--20549006	16	3.3	16	78	0	52	32	1	7	58	1.37
20556017--20556075	17	3.6	17	81	4	59	38	35	18	6	1.78
20569071--20569665	44	13.8	44	70	13	317	28	19	23	28	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20569076--20569282	84	2.4	87	79	11	212	30	20	22	26	1.98
20569075--20569632	217	2.6	217	89	0	848	29	19	22	28	1.98
20571262--20571304	18	2.4	18	84	7	52	32	4	4	58	1.39
20575664--20575704	21	2.0	21	100	0	82	26	14	29	29	1.95
20575796--20575927	6	22.0	6	93	0	192	18	3	15	61	1.49
20578342--20578367	11	2.4	11	100	0	52	50	7	42	0	1.31
20579088--20579175	39	2.2	40	84	9	110	36	7	18	37	1.80
20579350--20579525	45	4.2	39	75	17	149	19	19	21	39	1.93
20579377--20579527	45	3.3	45	89	0	221	19	18	21	40	1.92
20580083--20580124	22	1.9	22	85	0	57	38	0	23	38	1.55
20580830--20580878	24	2.0	25	96	4	91	12	0	30	57	1.36
20580854--20580984	69	1.9	69	90	4	212	22	7	19	50	1.72
20580932--20581029	29	3.6	29	71	15	93	28	7	12	52	1.65
20580932--20581029	27	3.7	26	76	9	99	28	7	12	52	1.65
20583376--20583407	8	4.0	8	100	0	64	62	0	0	37	0.95
20583372--20583413	16	2.6	17	88	11	70	61	0	0	38	0.96
20584105--20584156	21	2.5	21	84	6	70	36	40	13	9	1.77
20586486--20586564	26	3.2	25	76	15	83	34	18	26	20	1.96
20588298--20588360	3	21.3	3	73	15	51	0	34	0	65	0.93
20588298--20588345	21	2.3	21	86	10	64	0	39	0	60	0.97
20589528--20589591	27	2.4	27	78	0	65	48	3	3	45	1.34
20589678--20589732	27	2.2	24	84	12	67	21	0	16	61	1.34
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20590205--20590267	13	4.8	13	76	0	63	38	22	6	33	1.79
20592502--20592692	98	1.9	98	89	0	292	27	10	24	38	1.88
20603983--20604038	27	2.1	27	83	9	71	7	16	1	75	1.11
20605197--20605257	5	12.0	5	86	10	88	77	0	0	22	0.78
20605178--20605257	41	2.0	41	87	9	119	72	1	0	26	0.92
20609806--20609830	7	3.6	7	100	0	50	44	0	0	56	0.99
20618201--20618233	9	3.8	9	84	8	50	24	12	24	39	1.89
20618198--20618235	17	2.2	17	100	0	76	21	10	21	47	1.80
20618940--20618999	30	2.0	31	86	3	86	40	0	40	20	1.52
20619461--20619591	51	2.6	49	79	9	140	46	0	1	51	1.10
20621762--20621820	4	14.8	4	100	0	118	50	23	0	25	1.49
20621859--20621921	26	2.5	26	89	2	92	31	19	22	26	1.97
20628105--20628131	2	13.5	2	100	0	54	48	0	0	51	1.00
20629299--20629341	20	2.2	20	87	8	61	48	0	2	48	1.14
20629459--20629509	23	2.3	22	80	12	59	41	1	1	54	1.22
20629902--20630188	112	2.6	112	78	6	321	31	20	22	25	1.98
20630236--20630793	229	2.4	227	76	6	550	32	18	23	25	1.97
20630213--20630795	115	5.1	113	72	8	434	31	18	23	27	1.97
20632053--20632149	21	4.4	21	79	13	97	38	17	42	2	1.61
20632087--20632146	12	5.2	12	78	11	72	41	18	38	1	1.60
20632581--20632914	42	7.9	42	82	5	254	25	20	20	33	1.97
20632581--20632916	85	4.0	84	83	5	380	25	21	20	33	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20642058--20642133	27	2.8	27	82	7	91	30	25	15	28	1.96
20645778--20645811	15	2.3	15	94	0	59	32	32	17	17	1.94
20653494--20653574	25	3.2	25	70	13	76	37	27	13	22	1.91
20658331--20658361	16	1.9	16	93	0	53	32	25	16	25	1.96
20671033--20671108	31	2.5	30	78	19	77	32	14	5	47	1.67
20671279--20671352	25	3.0	25	70	16	73	31	17	27	24	1.97
20671247--20671352	50	2.1	49	86	5	142	29	19	24	26	1.99
20675203--20675280	28	2.7	29	76	2	77	34	28	12	24	1.92
20684494--20684566	26	2.8	26	75	2	76	17	27	21	32	1.96
20684530--20684610	25	3.3	25	70	13	60	19	29	19	30	1.97

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