genome.fa.s7.2.7.7.80.10.50.1000.180.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  180  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)
53176921--53176959	20	2.0	20	84	0	51	41	5	35	17	1.72
53179180--53179229	21	2.4	21	76	10	57	30	34	10	26	1.89
53183707--53183760	27	2.0	27	81	0	63	53	1	0	44	1.11
53184837--53184876	21	1.9	21	84	0	53	37	0	0	62	0.95
53185233--53185258	2	13.0	2	100	0	52	50	0	0	50	1.00
53188513--53188572	3	20.0	3	100	0	120	66	0	0	33	0.92
53189204--53189259	28	2.0	28	96	0	103	19	35	8	35	1.83
53192644--53192693	22	2.3	21	82	3	64	64	0	4	32	1.12
53195310--53195360	17	2.8	18	80	14	61	54	1	5	37	1.36
53196410--53196447	18	2.1	18	85	9	51	76	0	13	10	1.02
53197885--53197925	17	2.5	17	88	7	59	39	2	14	43	1.59
53197916--53197943	2	14.0	2	100	0	56	50	0	0	50	1.00
53198538--53198646	37	3.1	37	81	5	118	30	6	25	37	1.81
53208234--53208266	15	2.1	16	88	5	50	45	0	0	54	0.99
53208736--53208827	40	2.3	39	92	3	139	65	1	2	31	1.12
53208736--53208819	39	2.1	40	95	2	152	63	1	2	33	1.15
53210329--53210390	29	2.1	30	82	11	74	59	1	1	37	1.17
53227135--53227165	3	10.3	3	100	0	62	67	0	0	32	0.91
53236180--53236205	5	5.2	5	100	0	52	38	19	0	42	1.51
53236540--53236571	2	16.0	2	100	0	64	50	0	0	50	1.00
53242316--53242358	17	2.4	19	84	11	63	44	2	0	53	1.13
53242329--53242366	18	2.1	18	85	9	51	44	0	0	55	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53242807--53242851	22	2.0	23	82	4	56	26	6	13	53	1.64
53248114--53248144	2	15.5	2	100	0	62	48	0	0	51	1.00
53249134--53249174	17	2.4	17	87	4	55	60	2	0	36	1.10
53249243--53249315	38	1.9	38	82	0	92	54	2	10	31	1.49
53250041--53250075	18	1.9	18	94	0	61	65	2	0	31	1.07
53250041--53250076	19	1.9	18	88	5	54	66	2	0	30	1.06
53267179--53267398	43	5.3	42	80	7	236	30	30	17	20	1.96
53267285--53267356	36	2.0	36	91	0	117	26	34	16	22	1.95
53271922--53271957	14	2.6	13	87	12	54	33	47	0	19	1.50
53272907--53273148	41	5.9	41	92	0	403	28	28	20	21	1.98
53273135--53273251	40	3.0	40	84	2	148	24	17	18	39	1.92
53276248--53276300	16	3.3	16	74	10	54	37	24	5	32	1.79
53276491--53276617	41	3.2	41	84	5	156	32	22	19	25	1.98
53276799--53276832	2	17.0	2	100	0	68	50	0	0	50	1.00
53277504--53277533	15	1.9	16	93	6	53	0	20	0	80	0.72
53277506--53277543	19	2.0	19	85	10	51	0	23	2	73	0.95
53279762--53279805	18	2.4	18	81	7	54	43	15	0	40	1.47
53280070--53280125	14	3.8	14	75	13	58	1	25	3	69	1.14
53280099--53280142	22	2.0	22	82	4	54	2	18	2	77	0.98
53280109--53280156	9	5.3	9	83	16	55	6	14	0	79	0.92
53280655--53281055	210	1.9	208	84	3	529	23	16	13	45	1.84
53285451--53285480	16	1.9	16	93	6	53	50	3	6	40	1.45
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53293846--53293884	21	2.0	20	90	10	62	41	30	2	25	1.69
53295923--53295952	8	3.8	8	95	0	51	60	3	0	36	1.14
53305905--53305957	20	2.6	20	78	3	61	37	0	0	62	0.96
53306796--53306830	2	17.5	2	100	0	70	48	0	0	51	1.00
53307965--53308016	4	12.8	4	80	11	61	25	3	0	71	1.03
53309175--53309237	2	31.5	2	96	0	117	0	47	0	52	1.00
53309315--53309520	85	2.4	85	100	0	412	38	22	15	23	1.92
53311490--53311574	22	3.9	22	85	0	98	30	14	27	28	1.95
53312331--53312359	9	3.2	9	100	0	58	41	0	0	58	0.98
53320754--53320786	2	16.5	2	100	0	66	48	0	0	51	1.00
53328954--53329012	13	4.5	13	81	12	59	42	15	1	40	1.57
53328965--53329100	40	3.4	39	78	7	141	34	16	2	46	1.62
53329044--53329124	13	6.2	13	73	2	72	34	20	2	41	1.66
53328965--53329117	80	1.9	78	80	5	173	34	16	3	45	1.64
53328954--53329124	27	6.5	26	71	9	87	35	17	3	43	1.66
53333353--53333390	16	2.4	16	90	0	58	47	2	7	42	1.46
53333324--53333379	22	2.5	23	82	2	69	51	1	1	44	1.22
53333383--53333582	59	3.1	65	86	11	288	41	5	8	45	1.57
53333649--53333694	24	1.9	24	86	8	67	58	2	0	39	1.10
53337918--53339574	213	7.8	212	92	2	2256	33	21	17	28	1.95
53337918--53339574	639	2.6	638	90	2	2508	33	21	17	28	1.95
53344547--53344688	68	2.1	66	92	2	230	45	9	4	40	1.57
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53344677--53344718	16	2.6	16	92	0	66	42	7	2	47	1.43
53344692--53344747	23	2.5	23	82	2	69	44	1	1	51	1.22
53345532--53345632	47	2.1	47	100	0	202	44	9	17	27	1.81
53355795--53355829	2	18.5	2	88	11	56	48	0	0	51	1.00
53356244--53356297	15	3.1	18	82	15	60	61	1	0	37	1.07
53358897--53358945	20	2.4	21	90	6	75	32	2	8	57	1.40
53359328--53359386	32	1.9	32	86	6	86	37	1	1	59	1.18
53359355--53359394	18	2.2	19	86	4	55	35	0	0	65	0.93
53360888--53360942	16	3.1	18	87	10	69	60	1	0	38	1.08
53372221--53372254	3	11.3	3	100	0	68	64	0	35	0	0.94
53373763--53373787	13	1.9	13	100	0	50	64	0	0	36	0.94
53377579--53377625	24	2.0	24	91	0	76	38	2	8	51	1.45
53378694--53378731	17	2.2	17	100	0	76	28	10	10	50	1.70
53379553--53379602	13	3.8	13	79	10	66	34	2	24	40	1.66
53380084--53380108	13	1.9	13	100	0	50	36	16	16	32	1.90
53385614--53385662	11	4.1	12	82	12	57	2	6	10	81	0.94
53386678--53386746	12	5.8	12	80	16	58	69	0	4	26	1.07
53386717--53386746	3	10.0	3	100	0	60	66	0	0	33	0.92
53391344--53391393	27	1.9	25	84	8	64	16	10	22	52	1.73
53395234--53395372	71	2.0	71	89	0	215	36	27	5	30	1.80
53396248--53396306	25	2.3	27	82	11	70	44	15	1	38	1.56
53396273--53396313	13	3.0	14	73	20	50	36	14	2	46	1.58
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53396338--53396418	13	6.2	13	73	2	72	34	20	2	41	1.66
53397550--53397602	19	2.9	19	66	23	51	54	15	1	28	1.51
53398738--53398788	25	2.0	25	96	0	93	49	5	15	29	1.68
53399064--53399098	17	1.9	19	88	11	56	42	0	5	51	1.25
53399749--53400030	154	1.9	147	89	6	440	30	18	18	31	1.96
53400847--53400878	15	2.1	15	94	5	55	71	0	0	28	0.86
53401013--53401048	18	1.9	19	88	5	56	36	0	0	63	0.94
53401013--53401066	18	3.1	18	80	17	53	35	0	0	64	0.94
53406021--53407685	213	7.8	211	89	2	2356	33	21	17	27	1.95
53423553--53423612	19	3.1	19	79	13	68	56	1	3	38	1.26
53426356--53426383	6	4.7	6	100	0	56	0	64	0	35	0.94
53427711--53427755	22	2.0	22	82	0	54	53	4	2	40	1.33
53438029--53438088	24	2.7	22	85	10	79	33	38	6	21	1.80
53438029--53438080	24	2.2	24	96	0	95	36	36	5	21	1.77
53438651--53438831	25	7.3	25	84	5	215	31	1	18	48	1.58
53438651--53438833	41	4.4	41	77	12	155	31	1	19	47	1.59
53438658--53438833	9	21.0	9	76	12	153	31	1	19	47	1.60
53444539--53444854	9	37.4	9	79	11	323	30	2	20	46	1.64
53444532--53444854	25	12.8	27	81	8	278	30	2	20	47	1.63
53444539--53444854	34	9.4	34	79	8	237	30	2	20	46	1.64
53444852--53444893	21	2.0	21	90	0	66	52	0	0	47	1.00
53447096--53447130	18	1.9	19	88	11	56	34	2	0	62	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
53447083--53447178	30	3.3	29	75	17	83	39	5	0	55	1.22
53447173--53447231	30	2.0	30	83	6	75	52	1	3	42	1.28
53453001--53453035	2	17.5	2	93	0	61	48	0	2	48	1.16
53458366--53458435	6	11.7	6	98	0	131	17	1	15	65	1.34
53461027--53461070	21	2.1	21	84	16	56	54	0	6	38	1.27
53462026--53462059	16	2.1	17	88	5	52	76	5	0	17	0.98
53465101--53465129	11	2.6	11	100	0	58	68	0	17	13	1.20
53466746--53467390	28	24.2	28	83	11	786	46	20	0	32	1.54
53466746--53467389	51	12.1	51	82	11	583	46	20	0	32	1.54
53466743--53467373	79	7.9	79	86	7	848	45	20	0	33	1.54

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