genome.fa.s4.2.7.7.80.10.50.1000.32.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: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

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   188   189   190   191   192   
          193   194   195   196   197   198   

This is table  32  of  198  ( 23681 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)
9287602--9287689	29	3.0	29	77	11	81	29	19	21	29	1.98
9287618--9287667	14	3.5	14	75	5	55	30	22	18	30	1.97
9287678--9287739	23	2.7	24	82	5	65	29	14	22	33	1.94
9287799--9288094	34	8.7	33	82	5	349	33	19	17	30	1.95
9287799--9288094	102	2.9	102	86	3	389	33	19	17	30	1.95
9289565--9289597	15	2.2	15	94	0	57	66	0	0	33	0.92
9289827--9289870	22	2.0	23	86	13	65	38	0	4	56	1.20
9289942--9289984	20	2.2	20	87	8	61	53	0	9	37	1.33
9289943--9289984	11	4.1	11	79	17	54	54	0	7	38	1.28
9289997--9290037	19	2.2	19	95	0	73	46	0	24	29	1.53
9298936--9298980	23	2.0	22	83	12	56	44	4	8	42	1.56
9302873--9302897	2	12.5	2	100	0	50	48	0	0	52	1.00
9303339--9303396	11	5.7	10	80	6	55	77	5	3	13	1.07
9306804--9306838	2	17.5	2	100	0	70	51	0	0	48	1.00
9309493--9309533	17	2.3	18	80	12	50	48	0	4	46	1.23
9310245--9310456	40	5.3	39	65	15	99	19	19	8	53	1.69
9310271--9310469	20	9.9	20	67	14	97	19	20	9	50	1.75
9310882--9310950	21	3.4	19	79	15	77	18	17	5	57	1.59
9310871--9310981	20	5.5	20	69	14	75	18	18	9	53	1.72
9310886--9310973	40	2.1	42	85	4	117	19	15	7	56	1.63
9314091--9314131	20	2.0	20	85	0	55	24	7	7	60	1.48
9317082--9317111	13	2.3	13	94	0	51	30	10	10	50	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9317440--9317492	18	2.9	18	71	0	52	39	3	43	13	1.62
9317731--9317763	11	3.1	11	91	4	50	51	0	0	48	1.00
9323613--9323694	35	2.3	36	77	6	96	8	25	14	51	1.71
9324931--9324984	21	2.5	22	82	8	76	40	18	27	12	1.87
9324947--9324994	21	2.3	21	85	0	60	39	16	27	16	1.90
9330993--9331024	15	2.1	16	94	5	57	46	28	6	18	1.73
9337204--9337240	3	12.3	3	100	0	74	67	0	0	32	0.91
9339761--9339830	3	23.3	3	91	0	113	65	1	2	30	1.15
9345924--9345977	27	2.1	25	89	6	81	64	7	5	22	1.40
9346675--9348013	81	16.6	81	79	6	1326	30	19	23	27	1.98
9346767--9348013	162	7.7	162	93	1	1995	30	19	23	26	1.98
9348755--9348846	47	2.0	47	97	0	175	22	23	19	33	1.97
9352922--9353565	325	2.0	326	98	0	1245	32	18	14	34	1.91
9357617--9357910	99	3.0	98	93	2	489	19	37	12	30	1.89
9377551--9377590	5	8.0	5	88	0	62	45	0	0	55	0.99
9381513--9381552	20	2.0	20	85	0	53	37	10	0	52	1.35
9396366--9396430	22	3.0	22	83	0	85	35	23	0	41	1.55
9396441--9396479	21	1.9	20	85	15	53	35	30	0	33	1.58
9396524--9396580	30	1.9	30	89	10	91	36	0	1	61	1.07
9396679--9396712	15	2.3	15	90	5	52	26	0	5	67	1.13
9398532--9399501	29	32.8	29	85	8	1273	45	24	0	29	1.58
9398610--9399535	57	15.7	57	85	9	1107	45	24	0	29	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9398671--9398770	23	3.9	23	73	25	92	44	23	1	32	1.60
9399092--9399134	23	2.0	20	95	4	59	48	20	0	30	1.50
9398532--9399531	323	3.0	321	89	6	1428	45	25	0	29	1.58
9399436--9399477	22	1.9	22	100	0	84	42	23	0	33	1.55
9399458--9399531	36	2.1	34	90	5	112	43	29	0	27	1.55
9402937--9402988	24	2.2	24	85	0	68	53	5	3	36	1.43
9404889--9404940	24	2.2	24	89	0	77	53	9	3	32	1.51
9405662--9405696	2	17.5	2	100	0	70	48	0	0	51	1.00
9406122--9406188	22	3.4	22	67	26	67	32	14	10	41	1.80
9406090--9406186	37	2.6	37	91	0	149	32	16	8	42	1.78
9407105--9407129	11	2.3	11	100	0	50	40	8	0	52	1.31
9407127--9407199	9	7.4	9	74	19	58	27	1	0	71	0.95
9407145--9407195	11	4.5	11	76	13	59	31	1	0	66	1.03
9407115--9407213	51	1.9	51	97	0	189	33	2	0	64	1.05
9407155--9407249	41	2.2	40	87	9	127	33	2	0	64	1.06
9407105--9407243	51	2.7	50	86	7	174	32	2	0	64	1.08
9415935--9415993	30	2.0	29	87	12	84	3	54	1	40	1.27
9426243--9426287	22	2.0	22	95	0	81	26	33	13	26	1.93
9428915--9428945	16	2.0	16	93	6	55	48	6	0	45	1.28
9429709--9429752	21	2.1	21	100	0	88	36	31	13	18	1.90
9436506--9436548	22	2.0	22	81	9	52	60	11	6	20	1.54
9438586--9438623	2	19.0	2	100	0	76	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9439505--9439552	2	24.0	2	100	0	96	50	0	50	0	1.00
9440191--9440229	20	1.9	21	94	5	71	30	10	0	58	1.31
9447168--9447459	114	2.6	114	88	0	413	24	21	25	27	1.99
9447850--9447888	17	2.5	15	88	12	53	25	5	28	41	1.77
9449446--9449531	7	11.9	7	75	7	64	20	0	44	34	1.52
9449448--9449546	22	4.5	22	79	11	89	22	0	43	34	1.53
9449457--9449546	15	6.2	14	74	17	69	22	0	42	35	1.54
9449770--9449808	10	3.6	10	81	18	51	51	2	0	46	1.14
9449923--9450128	103	2.0	103	87	1	299	48	12	11	28	1.75
9452059--9452183	20	6.2	20	70	20	64	46	8	0	45	1.32
9452050--9452132	42	2.0	42	83	9	107	45	3	0	50	1.19
9452147--9452403	9	29.9	9	68	16	125	44	19	2	33	1.65
9452134--9452194	20	3.1	20	83	6	72	49	14	0	36	1.44
9452155--9452390	25	9.6	25	71	9	137	45	19	2	32	1.64
9452176--9452400	50	4.4	50	75	9	213	44	20	3	32	1.67
9453925--9453975	21	2.4	21	86	0	66	35	15	45	3	1.65
9454405--9454527	40	3.0	40	90	5	192	26	21	22	30	1.99
9454406--9454527	43	3.0	41	93	3	201	25	21	22	30	1.99
9455008--9455126	40	3.0	40	78	1	132	36	19	21	23	1.95
9455010--9455142	40	3.4	39	76	4	126	36	20	22	21	1.96
9455164--9455396	41	5.7	41	90	3	330	20	22	26	30	1.98
9455959--9455997	21	1.9	21	89	5	62	20	0	41	38	1.53
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9455958--9455991	14	2.4	14	90	9	52	17	0	44	38	1.49
9455979--9456228	89	2.8	89	96	0	464	26	0	26	46	1.58
9472208--9472237	15	2.0	15	100	0	60	46	6	0	46	1.29
9473888--9473983	21	4.4	21	78	10	86	37	15	41	5	1.70
9473947--9473980	12	2.8	12	95	0	59	47	8	38	5	1.59
9474417--9474711	42	7.0	40	84	9	315	25	22	21	31	1.98
9474418--9474710	127	2.3	128	88	4	425	24	22	21	31	1.98
9474415--9474728	85	3.7	84	85	6	395	25	22	21	30	1.99
9477328--9477408	40	2.0	40	83	6	103	37	3	7	51	1.48
9478753--9478829	29	2.6	29	83	4	91	46	14	14	24	1.81
9480795--9480852	11	5.4	11	74	12	57	37	5	0	56	1.21
9480786--9480860	32	2.4	31	89	6	116	34	4	0	61	1.15
9480795--9480878	43	2.0	43	85	4	116	35	3	1	59	1.22
9481137--9481231	49	1.9	49	81	12	115	43	28	4	24	1.73
9482053--9482295	44	5.7	43	76	6	208	28	21	20	30	1.98
9482141--9482295	42	3.7	42	81	9	158	29	21	20	27	1.98
9482013--9482297	127	2.2	129	86	3	380	28	22	20	29	1.98
9482304--9482573	50	5.4	50	73	2	220	26	24	19	30	1.98
9482304--9482612	100	3.1	100	88	3	453	25	24	20	29	1.99
9482330--9482620	50	5.8	50	72	1	217	25	24	20	29	1.99
9482691--9482797	50	2.1	50	81	6	119	26	27	21	25	1.99
9482809--9482987	88	2.0	88	88	2	261	24	26	22	26	2.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9484230--9484272	13	3.1	13	86	10	50	11	18	0	69	1.17
9484743--9484779	16	2.2	16	90	4	56	0	8	8	83	0.80
9484775--9484827	22	2.5	22	82	11	58	1	16	1	79	0.92
9484743--9484826	27	3.3	26	78	15	95	1	14	4	79	0.95
9484767--9484834	27	2.5	27	83	7	75	1	14	4	79	0.96
9484897--9484930	14	2.4	14	90	0	50	29	29	11	29	1.92
9487190--9487264	25	3.0	25	68	1	71	33	20	22	24	1.97
9487274--9487344	25	2.8	25	78	0	79	42	16	23	16	1.89
9487274--9487364	25	3.6	25	73	8	69	39	17	26	16	1.91
9487506--9487556	22	2.3	23	80	10	61	54	21	0	23	1.44

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   188   189   190   191   192   
          193   194   195   196   197   198