genome.fa.s8.2.7.7.80.10.50.1000.141.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   

This is table  141  of  190  ( 22705 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)
41572401--41572695	44	6.7	45	75	8	180	29	19	23	27	1.98
41573525--41573549	13	1.9	13	100	0	50	12	0	0	88	0.53
41574521--41574555	14	2.6	13	86	8	52	40	0	8	51	1.33
41575970--41576110	29	4.9	29	77	2	131	17	2	24	56	1.54
41578348--41578440	29	3.3	29	76	18	90	32	1	6	60	1.29
41578454--41578536	36	2.4	33	80	13	87	36	2	1	60	1.18
41578348--41578569	10	24.0	9	68	18	111	34	2	3	59	1.27
41579292--41579326	2	17.5	2	100	0	70	51	0	0	48	1.00
41587369--41587411	22	2.0	22	91	8	72	27	2	0	69	1.00
41587371--41587415	20	2.1	22	88	8	67	35	2	0	62	1.08
41599547--41599640	3	31.7	3	97	2	181	32	0	0	67	0.91
41603093--41603130	19	2.0	20	84	5	51	60	15	0	23	1.35
41605875--41606136	99	2.6	99	83	6	242	28	10	22	37	1.88
41605945--41606141	99	2.0	99	91	0	322	28	11	24	36	1.90
41617542--41618474	44	21.2	44	65	8	297	30	20	24	24	1.99
41617530--41618424	132	6.8	132	95	0	1520	30	20	25	24	1.99
41618415--41618536	44	2.8	43	76	8	131	31	20	19	27	1.97
41619485--41619521	19	1.9	19	94	0	65	43	0	13	43	1.44
41620410--41620606	99	2.0	99	92	0	331	27	10	25	36	1.89
41621273--41621450	96	1.9	96	81	7	218	49	3	1	45	1.28
41622869--41623015	73	2.0	73	87	0	213	36	7	14	40	1.75
41625939--41626024	25	3.4	25	70	12	68	18	29	19	32	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41625990--41626051	25	2.5	25	89	0	88	19	27	25	27	1.99
41628165--41628325	42	3.8	42	85	4	200	31	13	26	29	1.93
41628165--41628324	85	1.9	84	83	6	207	31	13	25	30	1.93
41636186--41636238	20	2.7	20	93	0	79	47	3	7	41	1.50
41639531--41639570	21	1.9	21	100	0	80	27	25	20	27	1.99
41640120--41640161	19	2.2	19	86	0	57	45	0	30	23	1.53
41646578--41646642	16	4.1	16	95	0	121	36	4	36	21	1.74
41646622--41646718	44	2.2	45	90	5	153	31	5	29	32	1.80
41647138--41647179	16	2.6	16	100	0	84	42	11	0	45	1.41
41651626--41651717	40	2.3	40	84	0	121	32	20	3	43	1.68
41651687--41651734	13	3.7	13	80	5	53	43	20	2	33	1.64
41651680--41651741	26	2.3	27	83	10	83	37	19	1	41	1.61
41653080--41653132	18	2.9	18	80	2	61	41	45	1	11	1.51
41653236--41653320	9	9.4	9	84	0	116	24	10	23	41	1.86
41668027--41668105	32	2.5	32	84	10	108	31	20	17	30	1.96
41670079--41670130	19	2.7	19	88	5	70	53	5	0	40	1.25
41670210--41670234	8	3.1	8	100	0	50	64	0	0	36	0.94
41676912--41676941	2	15.0	2	100	0	60	50	0	50	0	1.00
41679857--41679898	18	2.3	19	80	12	52	9	40	33	16	1.81
41686672--41686697	10	2.6	10	100	0	52	23	0	0	76	0.78
41702400--41702449	2	26.5	2	88	11	79	52	0	0	48	1.00
41711038--41711108	31	2.3	31	82	2	90	29	7	12	50	1.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41712554--41712579	12	2.2	12	100	0	52	26	15	19	38	1.91
41720699--41720724	5	5.2	5	100	0	52	0	19	42	38	1.51
41723416--41723449	12	2.8	12	90	0	50	26	11	2	58	1.47
41723852--41723878	3	9.0	3	100	0	54	33	0	0	66	0.92
41725221--41725308	44	2.0	44	100	0	176	13	22	27	36	1.92
41727274--41727459	41	4.5	41	94	0	309	25	27	17	29	1.98
41727274--41727487	82	2.6	81	87	2	311	26	26	17	29	1.98
41727682--41727721	2	20.0	2	100	0	80	50	0	0	50	1.00
41730962--41731073	57	1.9	58	87	5	165	30	10	23	35	1.89
41730962--41731093	57	2.3	57	83	10	162	29	11	21	37	1.89
41731302--41731655	138	2.6	138	82	0	404	18	20	25	35	1.95
41731301--41731704	69	5.9	69	80	1	353	18	19	25	36	1.94
41731367--41731724	138	2.6	138	81	0	419	18	18	25	36	1.94
41733595--41733631	5	7.4	5	90	0	56	35	0	21	43	1.53
41735189--41735228	21	1.9	21	85	10	55	0	22	2	75	0.93
41749228--41749353	42	3.0	42	89	0	189	25	10	19	45	1.81
41750078--41750132	23	2.4	23	96	0	101	36	16	18	29	1.92
41751862--41751905	24	1.9	24	81	9	56	29	2	9	59	1.41
41752391--41752439	25	1.9	26	84	12	66	30	4	20	44	1.70
41753856--41753971	58	2.0	58	91	0	187	29	14	24	31	1.95
41755229--41755276	24	2.0	24	91	0	78	47	10	22	18	1.79
41755361--41755496	42	3.2	41	84	3	164	15	20	19	44	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41755361--41755474	21	5.4	21	68	3	77	15	21	19	43	1.87
41758764--41758829	3	22.0	3	100	0	132	33	0	0	66	0.92
41764645--41765303	50	13.4	50	74	7	559	26	19	21	32	1.97
41764651--41765941	96	13.3	96	93	2	1425	23	20	23	32	1.98
41766246--41766332	44	2.0	44	93	0	147	39	24	10	26	1.87
41767078--41767178	43	2.3	44	83	9	120	29	22	14	32	1.94
41767256--41767290	12	3.0	11	88	12	52	0	11	2	85	0.69
41768442--41768481	6	6.3	6	91	5	53	5	20	0	75	0.99
41768438--41768488	19	2.5	20	78	12	59	5	23	0	70	1.09
41768508--41768552	6	7.8	6	87	7	67	0	0	15	84	0.62
41768499--41768551	24	2.2	24	83	3	63	3	1	13	81	0.92
41772179--41772205	7	3.9	7	100	0	54	59	0	0	40	0.98
41772424--41772459	17	2.1	17	100	0	72	30	0	16	52	1.44
41772428--41772475	17	2.7	17	87	6	60	37	0	12	50	1.41
41772526--41772559	3	11.3	3	100	0	68	67	32	0	0	0.91
41772558--41772591	3	11.3	3	100	0	68	67	0	0	32	0.91
41774165--41774192	4	7.0	4	100	0	56	25	0	25	50	1.50
41778666--41778871	101	2.0	101	96	0	376	33	18	16	31	1.93
41784356--41784385	15	2.0	15	93	0	51	43	0	0	56	0.99
41784666--41784690	12	2.1	12	100	0	50	24	0	0	76	0.80
41785981--41786021	21	2.0	21	85	0	55	43	0	0	56	0.99
41785978--41786027	21	2.4	21	75	15	50	44	0	0	56	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41786053--41786092	17	2.2	19	86	13	57	60	0	0	40	0.97
41786114--41786165	26	2.0	27	84	3	70	53	1	1	42	1.23
41786108--41786148	22	1.9	21	85	5	55	51	2	0	46	1.14
41786166--41786208	22	2.0	22	86	9	61	44	0	2	53	1.13
41793234--41793261	14	2.0	14	100	0	56	50	0	21	28	1.49
41798284--41798308	3	8.3	3	100	0	50	32	68	0	0	0.90
41800679--41800726	20	2.3	21	85	7	62	56	0	6	37	1.25
41802733--41802771	20	2.0	20	89	0	60	30	25	35	7	1.84
41804464--41804503	6	6.5	6	91	2	62	0	62	0	37	0.95
41811372--41811405	14	2.5	14	95	4	61	14	0	35	50	1.44
41811534--41811580	24	1.9	25	82	4	60	68	6	6	19	1.34
41813512--41813576	27	2.4	27	75	17	71	12	10	3	73	1.20
41820175--41820218	22	2.0	21	87	12	63	54	9	0	36	1.32
41821089--41821158	2	35.0	2	100	0	140	50	50	0	0	1.00
41832298--41832359	26	2.4	26	88	0	97	35	12	12	38	1.82
41832568--41832600	17	1.9	17	100	0	66	42	9	0	48	1.35
41841219--41841248	13	2.3	13	94	0	51	23	10	13	53	1.69
41841697--41841742	21	2.2	21	80	7	58	54	4	0	41	1.20
41844918--41844966	9	5.4	9	95	0	89	42	22	10	24	1.84
41845036--41845064	6	4.8	6	100	0	58	17	0	17	65	1.27
41845021--41845077	18	2.9	20	82	12	64	22	3	12	61	1.46
41852073--41852097	2	12.5	2	100	0	50	52	48	0	0	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
41855695--41855738	20	2.1	21	87	4	63	68	0	2	29	1.02
41858094--41858128	19	1.9	18	88	11	54	60	2	2	34	1.26
41858098--41858190	25	3.7	26	75	8	84	51	6	7	34	1.56
41858228--41858271	15	3.1	15	90	6	65	72	0	0	27	0.85
41858228--41858271	13	3.5	13	81	12	56	72	0	0	27	0.85
41860010--41860050	21	1.9	22	90	5	66	68	4	0	26	1.10
41860172--41860204	12	2.8	12	86	13	50	30	0	3	66	1.06
41862084--41862156	23	3.3	23	82	3	87	13	27	26	32	1.94
41863979--41864079	41	2.4	42	79	9	118	32	31	14	20	1.93
41874974--41875134	41	3.9	42	80	8	152	31	26	16	26	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   188   189   190