genome.fa.s7.2.7.7.80.10.50.1000.188.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: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  60982465

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   199   200   201   202   203   204   

This is table  188  of  204  ( 24458 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)
55467706--55467730	5	5.0	5	100	0	50	0	20	0	80	0.72
55480107--55480177	34	2.1	34	100	0	142	28	8	11	52	1.66
55486246--55486307	31	2.0	31	84	6	81	20	12	6	59	1.55
55487020--55487063	21	2.2	20	91	4	70	61	0	0	38	0.96
55487284--55487326	18	2.4	17	81	11	50	25	4	2	67	1.22
55487440--55487609	89	1.9	87	86	4	243	35	8	17	38	1.81
55489166--55489216	19	2.9	18	77	16	63	17	3	0	78	0.90
55498546--55498612	29	2.2	31	84	10	86	46	2	8	41	1.50
55506274--55506326	13	4.1	13	77	0	61	37	24	5	32	1.79
55511611--55511648	19	2.0	20	89	5	60	55	2	0	42	1.14
55512137--55512187	18	2.8	18	88	8	68	21	1	11	64	1.36
55512560--55512589	7	4.3	7	100	0	60	26	30	13	30	1.94
55518368--55518406	3	13.0	3	94	0	69	64	0	2	33	1.08
55520240--55520363	45	2.8	43	74	16	126	29	21	18	30	1.97
55520180--55520363	89	2.1	88	83	5	228	29	20	18	32	1.96
55520426--55520570	44	3.3	44	76	7	159	29	24	18	26	1.98
55520441--55520580	44	3.2	44	76	9	167	27	24	17	31	1.97
55532656--55532710	3	18.3	3	100	0	110	65	0	0	34	0.93
55533961--55534013	23	2.2	24	80	12	65	47	3	0	49	1.19
55534421--55534470	22	2.3	22	79	6	57	14	34	6	46	1.69
55536912--55536959	23	2.1	22	81	11	53	45	2	0	52	1.12
55537382--55537427	20	2.2	20	92	3	74	30	2	15	52	1.55
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55539072--55539195	60	2.1	60	100	0	248	37	8	14	39	1.76
55539678--55539711	17	1.9	18	88	5	52	50	0	0	50	1.00
55545836--55545867	2	16.0	2	93	0	55	46	0	0	53	1.00
55545832--55545875	18	2.5	18	82	17	65	40	0	4	54	1.21
55555623--55555661	21	1.9	19	90	10	60	23	30	7	38	1.83
55559768--55560294	155	3.4	153	85	6	669	30	17	9	42	1.81
55560348--55560378	16	1.9	16	100	0	62	45	16	0	38	1.47
55559769--55560476	305	2.3	307	80	11	731	30	17	9	43	1.79
55561875--55561917	22	2.0	21	86	8	61	39	0	0	60	0.97
55563062--55563167	37	2.8	36	83	7	122	16	18	10	53	1.71
55564843--55564876	17	1.9	18	88	5	52	50	0	0	50	1.00
55566723--55566841	64	1.9	63	92	1	202	27	14	21	36	1.92
55568856--55568894	21	1.9	19	90	10	60	23	30	7	38	1.83
55572717--55572742	2	13.0	2	100	0	52	50	0	0	50	1.00
55580735--55580760	9	2.9	9	100	0	52	34	11	7	46	1.69
55581179--55581220	20	2.2	19	87	12	59	21	30	7	40	1.80
55591335--55591368	5	7.2	5	87	12	54	41	0	0	58	0.98
55591333--55591368	9	3.9	9	92	7	63	41	0	0	58	0.98
55591461--55591519	3	19.7	3	100	0	118	33	0	0	66	0.92
55591598--55591623	5	5.2	5	100	0	52	19	0	0	80	0.71
55594513--55594573	29	2.1	29	100	0	122	42	6	18	32	1.76
55594513--55594588	29	2.6	29	89	4	91	43	6	15	34	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55595526--55595601	39	1.9	39	97	0	143	36	11	15	35	1.85
55595625--55595692	31	2.2	31	84	7	95	48	11	1	38	1.49
55599334--55599754	143	2.9	144	94	2	709	26	18	10	44	1.82
55602385--55602432	20	2.4	21	75	10	55	31	29	14	25	1.95
55606155--55606193	21	1.9	19	90	10	60	23	30	7	38	1.83
55612694--55612747	19	2.6	21	82	11	67	33	12	3	50	1.59
55612694--55612752	21	2.9	21	82	10	68	33	13	3	49	1.59
55614810--55615340	159	3.5	151	83	5	636	30	17	8	43	1.79
55614810--55615340	153	3.5	150	84	4	632	30	17	8	43	1.79
55615541--55615574	2	17.0	2	100	0	68	50	0	0	50	1.00
55615705--55615754	26	2.0	25	84	4	64	32	8	24	36	1.84
55617456--55617500	18	2.4	19	81	3	56	20	26	8	44	1.80
55618154--55618304	37	4.1	37	85	0	194	19	16	12	50	1.76
55619222--55619289	33	2.1	33	97	0	127	51	4	32	11	1.58
55620433--55620467	17	2.1	17	100	0	70	51	0	20	28	1.47
55624081--55624122	20	2.2	19	87	12	59	21	30	7	40	1.80
55626189--55626254	33	2.0	33	96	0	123	18	16	9	56	1.66
55652779--55652819	19	2.2	20	83	12	52	19	4	14	60	1.51
55656131--55656455	109	3.0	109	88	3	442	36	18	14	30	1.91
55657201--55657275	3	25.7	3	90	8	111	68	0	2	29	1.04
55658766--55658812	23	2.1	22	88	7	69	44	0	0	55	0.99
55659204--55659284	36	2.3	36	87	6	121	25	28	8	37	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55659261--55659310	22	2.3	22	79	6	57	14	34	6	46	1.69
55661723--55661769	23	2.0	23	95	0	85	34	10	27	27	1.90
55662103--55662132	15	2.0	15	93	0	51	66	3	0	30	1.07
55662948--55663016	18	3.9	18	70	14	54	34	21	10	33	1.87
55672004--55672046	23	1.9	23	85	4	61	48	2	0	48	1.14
55672210--55672482	143	1.9	143	93	2	467	27	16	11	44	1.82
55674881--55674922	22	1.9	22	85	9	59	47	2	0	50	1.14
55682305--55682343	21	1.9	19	90	10	60	23	30	7	38	1.83
55687727--55687803	22	3.4	22	67	19	68	36	25	2	35	1.70
55687714--55687808	46	2.1	46	100	0	190	41	23	2	33	1.66
55689109--55689170	29	2.2	28	82	2	70	25	14	14	45	1.83
55689892--55689916	7	3.6	7	100	0	50	28	0	12	60	1.32
55691004--55691114	25	4.6	25	67	20	83	37	2	14	45	1.59
55691002--55691186	71	2.6	71	93	0	316	37	3	14	44	1.63
55691185--55691237	23	2.7	18	75	25	61	50	20	0	28	1.48
55691192--55691239	23	2.1	23	100	0	96	45	25	0	29	1.53
55691207--55691482	29	9.6	29	89	0	419	45	29	0	24	1.53
55691477--55691715	55	4.3	56	92	2	394	38	12	4	45	1.62
55691477--55691715	112	2.1	110	92	3	390	38	12	4	45	1.62
55691699--55691725	10	2.7	10	100	0	54	40	7	0	51	1.30
55691643--55691789	66	2.2	66	95	2	260	36	10	4	48	1.58
55694901--55695248	124	2.8	124	90	2	567	31	20	16	31	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55696302--55696437	39	3.4	39	75	14	143	44	7	0	47	1.36
55699161--55699274	37	3.1	37	87	1	156	20	16	11	51	1.75
55700743--55700776	17	1.9	18	88	5	52	50	0	0	50	1.00
55700948--55700998	20	2.5	20	81	6	59	33	35	13	17	1.89
55702353--55702391	21	1.9	19	90	10	60	23	30	7	38	1.83
55705960--55705989	15	2.0	15	100	0	60	60	0	13	26	1.34
55713166--55713206	21	2.0	21	85	0	55	24	0	29	46	1.53
55713344--55713382	15	2.5	16	84	16	55	61	0	2	35	1.10
55714067--55714109	17	2.4	19	84	7	63	32	44	2	20	1.65
55715360--55715397	17	2.2	17	86	9	51	31	5	5	57	1.43
55716695--55716984	144	2.0	144	100	0	580	39	10	8	41	1.71
55717103--55717154	20	2.6	20	87	0	68	50	3	5	40	1.45
55717167--55717405	9	27.9	9	72	13	175	45	18	1	34	1.58
55717340--55717412	32	2.2	33	85	9	96	47	17	2	31	1.62
55722395--55722465	21	3.4	21	88	0	106	30	18	46	4	1.68
55722787--55723068	42	6.7	42	87	1	377	32	22	21	22	1.98
55722812--55723105	126	2.3	127	84	2	333	32	22	21	23	1.98
55724430--55724483	21	2.7	20	86	11	67	37	16	1	44	1.59
55726277--55726310	2	17.0	2	100	0	68	50	0	0	50	1.00
55726858--55726899	2	21.0	2	100	0	84	50	0	0	50	1.00
55728787--55728822	19	1.9	18	88	5	54	61	8	2	27	1.39
55728845--55728888	7	5.9	7	80	15	52	36	0	0	63	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55730074--55730368	42	7.0	42	84	4	360	31	21	22	24	1.98
55730074--55730368	85	3.5	84	81	5	353	31	21	22	24	1.98
55730076--55730368	127	2.3	127	84	3	383	31	21	22	24	1.98
55734934--55734972	21	1.9	19	90	10	60	23	30	7	38	1.83
55768620--55768733	37	3.1	37	87	1	156	21	16	11	50	1.76
55775251--55775299	19	2.4	21	86	6	66	34	16	4	44	1.66
55775251--55775304	21	2.7	20	85	5	65	35	16	3	44	1.66
55777415--55778156	153	5.0	151	80	9	756	30	18	8	43	1.79
55777816--55778081	141	1.9	140	88	3	403	30	19	8	41	1.82
55778888--55778924	16	2.3	16	100	0	74	56	8	10	24	1.60

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   199   200   201   202   203   204