genome.fa.s1.2.7.7.80.10.50.1000.45.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  45  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)
13651613--13651758	47	3.2	46	67	20	124	46	4	2	45	1.38
13651625--13651832	91	2.3	91	93	0	344	46	4	3	46	1.39
13651628--13651767	44	3.1	43	65	17	104	45	4	2	47	1.37
13651650--13651792	44	3.2	43	68	16	119	48	3	2	46	1.31
13651675--13651813	47	3.0	47	68	17	137	49	4	2	43	1.34
13653241--13653267	11	2.5	11	100	0	54	51	18	7	22	1.70
13654828--13654893	33	2.0	33	96	0	123	36	6	13	43	1.69
13655108--13655194	37	2.4	37	94	0	147	35	8	14	41	1.76
13656113--13656164	26	2.0	26	100	0	104	34	19	11	34	1.88
13656391--13656453	23	2.7	23	83	16	94	53	22	7	15	1.67
13656380--13656656	107	2.6	107	91	0	455	45	23	7	23	1.77
13662114--13662170	5	11.4	5	100	0	114	40	0	0	59	0.97
13662182--13662253	18	3.7	19	74	20	60	69	4	26	0	1.06
13662909--13662963	24	2.2	26	78	18	64	36	0	20	43	1.52
13663121--13663261	40	3.5	39	71	10	115	24	17	24	34	1.96
13664401--13664507	28	3.8	28	71	7	83	56	6	4	32	1.46
13665343--13665370	14	2.0	14	100	0	56	57	7	7	28	1.52
13671447--13671600	76	2.0	76	96	0	281	27	22	16	33	1.95
13677252--13677296	2	22.5	2	95	0	81	46	0	2	51	1.13
13677908--13677958	21	2.4	21	90	0	75	27	15	21	35	1.94
13678232--13678278	21	2.2	21	85	7	60	40	23	12	23	1.89
13678329--13678405	34	2.3	34	88	4	111	41	16	14	27	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13679224--13679260	5	7.0	5	88	11	56	75	0	24	0	0.80
13679222--13679258	11	3.3	11	96	3	65	72	0	27	0	0.84
13679224--13679260	16	2.3	16	90	9	58	75	0	24	0	0.80
13688159--13688186	2	14.0	2	100	0	56	50	0	0	50	1.00
13696172--13696217	19	2.3	20	81	7	58	43	4	0	52	1.21
13696185--13696225	11	4.0	11	75	18	52	36	7	0	56	1.27
13696183--13696228	19	2.5	19	92	3	76	32	6	0	60	1.22
13696194--13696236	19	2.3	19	84	8	52	44	4	2	48	1.36
13700305--13700353	19	2.5	20	86	6	64	34	18	16	30	1.93
13701709--13701758	21	2.4	22	80	16	61	50	8	0	42	1.32
13706765--13706803	21	2.0	20	85	10	53	33	20	15	30	1.94
13713266--13713309	22	1.9	24	86	9	65	65	2	25	6	1.28
13726631--13726686	18	3.0	20	80	17	57	76	0	7	16	0.99
13726580--13726654	38	2.0	38	82	10	91	68	0	10	21	1.20
13726634--13726680	6	7.6	7	82	17	52	74	0	8	17	1.05
13726646--13726680	18	2.0	18	94	5	63	71	0	11	17	1.14
13729156--13729382	79	2.9	79	85	1	294	43	16	10	30	1.81
13738369--13738401	15	2.1	16	94	5	59	69	0	3	27	1.03
13741378--13741429	24	2.2	24	89	0	77	55	9	1	32	1.43
13748995--13749040	19	2.5	20	86	10	62	52	0	6	41	1.27
13751452--13751485	15	2.3	15	100	0	68	41	23	5	29	1.78
13755373--13755450	27	2.8	30	75	15	85	48	3	0	47	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13758163--13758289	3	42.3	3	92	3	211	0	30	0	68	0.95
13761687--13761722	16	2.2	16	90	0	54	2	11	5	80	0.98
13762097--13762123	14	1.9	14	100	0	54	44	7	11	37	1.68
13762217--13762254	14	2.8	13	92	7	67	47	5	10	36	1.61
13762507--13762685	34	5.3	34	83	5	227	17	24	15	42	1.88
13765491--13765535	20	2.1	23	88	12	69	13	8	8	68	1.38
13765568--13765610	21	2.0	23	81	9	54	32	11	11	44	1.77
13769678--13769708	5	6.0	5	96	3	53	0	58	41	0	0.98
13769770--13769835	17	3.6	17	83	15	87	65	0	0	34	0.93
13769783--13769841	9	6.3	9	77	14	66	72	0	0	27	0.84
13769787--13769824	11	3.5	11	85	7	60	68	0	0	31	0.90
13769767--13769824	10	5.9	10	71	17	50	63	0	0	36	0.94
13769783--13769824	21	2.0	21	100	0	84	71	0	0	28	0.86
13769733--13769878	38	3.7	37	80	14	136	63	0	2	33	1.09
13769838--13769862	11	2.3	11	100	0	50	52	0	8	40	1.31
13770142--13770177	17	2.1	17	100	0	72	50	16	16	16	1.79
13770508--13770551	23	1.9	23	100	0	88	31	15	31	20	1.94
13774779--13774873	9	10.2	9	67	17	52	66	2	1	30	1.10
13774827--13774873	20	2.4	19	82	6	58	68	0	2	29	1.02
13774779--13774873	19	5.1	18	71	9	75	66	2	1	30	1.10
13776559--13776636	39	2.0	38	85	7	104	29	10	14	46	1.77
13778343--13778367	2	12.5	2	100	0	50	52	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13779166--13779190	1	25.0	1	100	0	50	0	0	0	100	0.00
13779652--13779702	25	2.0	25	100	0	102	19	27	3	49	1.66
13780895--13780927	16	2.1	16	88	11	50	75	0	12	12	1.04
13785591--13785629	2	19.5	2	94	0	69	48	2	0	48	1.15
13786337--13786489	25	6.2	25	74	8	109	33	19	27	18	1.96
13786434--13786482	26	1.9	25	87	4	71	36	20	22	20	1.95
13788289--13789902	806	2.0	806	99	0	3201	38	10	15	34	1.83
13790370--13790691	161	2.0	161	94	1	565	34	22	14	28	1.93
13791362--13791506	71	2.0	71	87	0	209	42	22	20	15	1.89
13791430--13791646	117	1.9	117	86	3	312	44	23	16	15	1.86
13791421--13791672	117	2.1	117	81	8	296	42	23	17	16	1.88
13793997--13794031	14	2.5	14	90	0	52	11	8	14	65	1.46
13795642--13795799	17	8.7	17	69	22	74	46	1	2	49	1.23
13795625--13795699	12	6.6	12	70	21	54	45	0	2	52	1.15
13795627--13795763	45	2.9	46	71	19	120	45	0	2	51	1.21
13795625--13795700	20	4.0	19	81	11	84	44	0	2	52	1.14
13796579--13796609	7	4.4	7	91	0	53	9	0	41	48	1.36
13796643--13796924	124	2.3	124	88	1	422	28	18	22	30	1.97
13799953--13800118	37	4.4	38	63	17	94	42	7	9	40	1.65
13799928--13800198	114	2.4	114	96	0	506	42	7	9	40	1.67
13800206--13800713	21	24.2	21	84	2	581	25	1	27	45	1.61
13800973--13801019	21	2.2	21	85	7	60	2	23	36	38	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13803166--13803219	11	4.9	11	77	18	51	42	1	31	24	1.65
13803166--13803219	22	2.5	21	82	14	65	42	1	31	24	1.65
13815741--13815801	31	1.9	32	83	9	81	40	4	0	54	1.22
13815828--13815883	15	3.7	15	69	6	51	30	3	3	62	1.29
13824914--13824950	18	2.1	18	94	0	65	35	10	8	45	1.69
13828611--13828702	24	3.8	23	79	11	87	32	19	25	22	1.97
13828641--13828823	24	7.5	24	76	9	156	37	20	24	17	1.94
13828611--13828807	50	4.0	50	77	7	188	37	19	23	19	1.94
13828620--13828807	99	1.9	98	83	3	243	37	19	24	18	1.94
13833261--13833294	15	2.3	15	90	10	52	58	0	14	26	1.36
13834936--13835000	28	2.4	28	84	7	80	38	9	7	44	1.65
13840143--13840185	18	2.3	18	84	11	52	6	4	4	83	0.89
13840143--13840185	16	2.7	15	82	13	50	6	4	4	83	0.89
13840354--13840432	38	2.1	38	95	0	140	15	7	31	45	1.74
13842428--13842465	13	2.8	14	80	19	53	65	5	7	21	1.38
13842899--13842940	23	1.9	22	85	9	59	66	7	4	21	1.35
13844791--13844910	44	2.7	46	80	3	138	25	28	20	25	1.99
13844918--13845730	267	3.0	266	89	0	1241	26	25	20	27	1.99
13845809--13845972	44	3.7	44	90	1	240	29	25	17	28	1.97
13846848--13846896	25	1.9	26	87	4	73	61	10	12	16	1.57
13852346--13852388	23	2.0	22	86	9	61	65	6	6	20	1.41
13854214--13854515	148	2.0	150	92	1	500	23	28	20	27	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
13863062--13863099	15	2.5	15	91	0	58	18	5	0	76	0.97
13864133--13864172	21	1.9	21	89	0	62	40	0	20	40	1.52
13864756--13864835	25	3.2	25	82	1	90	17	27	21	33	1.96
13868958--13868988	16	1.9	16	100	0	62	32	6	3	58	1.40
13868982--13869032	24	2.3	23	81	15	63	41	0	0	58	0.98
13881266--13881324	28	2.1	28	90	0	91	30	23	23	22	1.99
13881424--13881478	26	2.1	26	89	0	83	34	23	21	20	1.97
13881672--13881783	27	4.2	27	84	5	138	20	14	19	45	1.85
13881672--13881783	54	2.1	53	88	5	163	20	14	19	45	1.85
13886912--13887004	28	3.0	33	72	18	90	27	21	24	25	1.99

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