genome.fa.s9.2.7.7.80.10.50.1000.200.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: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  70713020

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   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   

This is table  200  of  226  ( 27023 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)
63359915--63359983	22	3.1	22	67	8	68	49	13	2	34	1.56
63360047--63360116	22	3.2	21	64	8	50	47	12	1	38	1.51
63360275--63360360	36	2.4	36	82	2	109	23	30	26	19	1.98
63360532--63360610	23	3.5	20	70	28	52	62	0	12	25	1.31
63360537--63360619	26	3.4	25	75	21	102	62	0	14	22	1.31
63360555--63360594	20	2.0	20	85	9	55	62	0	12	25	1.30
63360797--63360849	25	2.1	25	85	0	70	49	0	11	39	1.39
63360847--63360893	22	2.2	21	81	11	51	68	2	6	23	1.24
63360854--63360893	21	1.9	21	85	10	55	70	2	5	22	1.19
63360932--63360976	16	2.9	15	87	9	54	66	0	11	22	1.22
63361063--63361140	5	14.4	5	74	15	66	51	0	19	29	1.47
63361063--63361140	16	4.8	15	77	13	66	51	0	19	29	1.47
63361063--63361151	28	3.2	28	80	12	112	50	0	19	30	1.48
63361225--63361273	21	2.4	19	77	12	53	67	0	14	18	1.23
63363551--63363599	25	1.9	25	87	4	71	55	2	4	38	1.31
63363777--63363836	3	20.0	3	89	6	95	66	1	0	31	1.01
63365983--63366398	90	4.6	90	91	1	624	52	15	7	24	1.68
63367059--63367275	111	2.0	111	90	3	348	31	23	18	25	1.98
63371101--63371157	27	2.0	29	86	6	82	50	5	3	40	1.42
63372754--63372810	27	2.2	25	84	9	71	36	12	7	43	1.69
63372746--63372801	27	2.1	27	93	0	94	37	16	8	37	1.80
63375660--63375730	22	3.2	22	66	15	65	39	14	21	25	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
63375658--63375767	44	2.5	44	98	1	211	40	13	22	23	1.90
63375680--63375749	22	3.2	22	65	15	63	42	14	21	21	1.88
63375698--63375768	22	3.2	23	65	15	67	39	12	23	23	1.89
63375790--63375840	21	2.4	22	72	21	54	39	17	17	25	1.92
63377851--63377878	9	3.1	9	100	0	56	32	21	21	25	1.98
63379891--63380240	50	6.8	50	82	3	358	27	21	28	22	1.99
63379947--63380221	102	2.7	102	93	1	446	27	22	28	21	1.99
63379955--63380289	152	2.2	150	82	3	395	27	22	28	22	1.99
63381700--63381771	31	2.3	31	83	4	83	31	15	5	47	1.68
63387568--63387637	35	2.0	35	88	5	106	50	21	14	14	1.78
63388429--63388471	2	21.5	2	100	0	86	51	0	0	48	1.00
63393354--63393382	4	7.2	4	100	0	58	75	0	0	24	0.80
63396771--63396822	16	3.0	18	83	10	56	55	1	0	42	1.10
63396792--63396845	16	3.4	15	78	17	56	51	0	0	48	1.00
63396789--63396849	30	2.0	31	87	9	90	50	0	0	49	1.00
63396799--63396851	16	3.2	16	75	21	56	49	0	0	50	1.00
63396897--63396923	13	2.1	13	100	0	54	40	0	0	59	0.98
63403599--63403702	37	2.8	37	78	16	110	44	2	2	50	1.32
63403646--63403700	25	2.2	24	84	12	67	47	1	3	47	1.30
63403730--63403805	32	2.3	33	81	4	91	46	0	2	51	1.15
63409225--63409268	22	2.0	23	90	4	72	36	4	18	40	1.71
63409225--63409283	22	2.7	23	81	5	68	32	3	18	45	1.66
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
63410050--63410086	9	4.1	9	92	0	65	45	13	10	29	1.77
63411188--63411217	6	5.0	6	100	0	60	16	50	0	33	1.46
63415524--63415685	33	4.8	33	69	25	113	33	29	20	17	1.95
63415526--63415755	103	2.2	103	96	0	424	32	30	20	17	1.96
63415693--63415798	43	2.5	43	96	0	194	32	29	16	22	1.95
63423136--63423285	33	4.4	33	68	26	107	34	30	19	16	1.93
63423264--63423317	27	2.0	28	96	3	101	25	33	24	16	1.96
63423367--63423418	27	1.9	27	92	0	86	28	32	23	15	1.95
63423126--63423433	103	3.0	103	94	1	519	32	28	18	19	1.96
63441062--63441094	14	2.4	14	100	0	66	36	12	15	36	1.84
63441746--63441787	18	2.2	20	87	8	61	47	9	11	30	1.72
63442219--63442252	17	1.9	17	88	5	50	17	35	29	17	1.93
63447601--63447665	29	2.2	29	91	2	103	41	38	3	16	1.64
63447601--63447681	30	2.7	29	88	7	110	41	39	2	16	1.61
63455215--63455282	25	2.7	26	78	15	79	17	25	22	35	1.95
63455215--63455282	26	2.7	25	84	6	84	17	25	22	35	1.95
63458906--63458959	27	2.0	27	100	0	108	18	11	22	48	1.79
63463034--63463105	26	2.8	25	77	4	90	18	29	23	29	1.97
63464113--63464145	13	2.5	13	100	0	66	24	42	21	12	1.86
63488271--63488337	33	2.0	33	100	0	134	17	26	29	25	1.98
63493845--63493912	29	2.3	29	89	2	100	20	23	33	22	1.97
63507074--63507100	4	6.8	4	100	0	54	22	0	0	77	0.76
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
63510322--63510357	18	2.0	18	94	0	63	22	13	16	47	1.82
63512291--63512407	44	2.7	44	76	11	114	32	26	16	24	1.96
63512829--63512872	15	3.1	14	80	12	54	43	6	0	50	1.29
63516844--63516918	24	3.2	23	75	15	82	45	1	0	53	1.08
63516852--63516914	22	2.6	26	80	12	71	46	1	0	52	1.10
63521119--63521155	19	2.1	19	90	10	60	56	2	10	29	1.47
63529395--63529431	19	2.0	19	89	5	58	35	0	8	56	1.29
63531029--63531063	16	2.2	16	89	0	52	34	17	5	42	1.73
63539593--63539636	23	1.9	22	82	17	54	36	25	2	36	1.69
63539681--63539774	45	2.1	45	88	4	136	30	23	18	27	1.97
63539771--63539957	51	3.7	51	78	2	198	32	27	16	24	1.96
63539777--63539965	101	1.9	99	82	5	236	33	27	15	23	1.95
63543454--63543734	138	2.0	138	92	1	465	45	7	7	39	1.61
63545797--63545839	3	14.3	3	100	0	86	67	0	0	32	0.91
63556703--63556778	23	3.3	23	94	0	134	31	25	21	22	1.98
63562079--63562130	24	2.0	26	82	10	63	51	5	0	42	1.25
63566714--63566750	17	2.2	17	90	0	56	21	43	21	13	1.87
63567566--63567608	22	2.0	22	90	9	70	46	20	9	23	1.79
63567855--63567891	18	2.0	19	89	5	58	45	29	0	24	1.53
63572860--63572894	16	2.2	16	89	0	52	34	0	31	34	1.58
63572935--63573050	61	1.9	61	91	3	189	53	1	0	43	1.16
63573071--63573157	24	3.6	24	74	10	70	42	2	2	52	1.26
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
63573091--63573157	23	2.9	23	76	10	73	40	2	2	53	1.31
63576314--63576354	15	2.8	15	85	10	50	41	9	0	48	1.36
63577765--63577862	18	5.0	18	78	20	99	0	54	7	38	1.28
63577765--63577893	21	6.3	21	76	12	108	0	55	7	35	1.34
63577765--63577889	39	3.1	41	86	8	145	0	56	7	36	1.33
63577783--63577851	24	3.0	24	87	6	90	0	55	8	36	1.31
63577768--63577889	63	1.9	63	83	6	158	0	55	6	36	1.32
63577765--63577893	42	3.2	40	82	11	147	0	55	7	35	1.34
63577942--63577984	18	2.4	18	84	0	50	4	41	9	44	1.57
63596863--63596902	16	2.5	17	88	8	57	32	0	2	65	1.06
63597195--63597227	17	1.9	17	93	0	57	18	21	33	27	1.96
63602787--63602825	20	2.0	20	89	0	60	35	2	0	61	1.10
63616065--63616114	2	25.0	2	100	0	100	50	0	0	50	1.00
63618289--63618530	44	5.6	44	79	8	257	28	23	18	29	1.97
63618369--63618447	38	2.1	38	85	0	104	27	24	15	32	1.95
63618325--63618490	82	2.0	82	87	2	235	28	24	16	30	1.97
63618286--63618512	126	1.8	126	95	0	409	29	24	15	30	1.96
63618541--63619028	88	5.5	88	91	1	782	20	25	27	27	1.99
63618599--63618996	44	9.1	43	62	5	141	19	25	28	26	1.99
63623819--63623849	6	5.3	6	92	7	55	83	0	0	16	0.64
63625130--63625155	2	13.0	2	100	0	52	50	0	0	50	1.00
63637016--63637078	27	2.3	27	94	0	108	23	26	12	36	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
63641195--63641219	8	3.1	8	100	0	50	0	24	52	24	1.48
63642531--63642566	8	4.4	8	89	3	54	25	11	2	61	1.43
63649133--63649388	67	3.8	67	93	0	431	39	1	17	41	1.60
63650692--63650716	13	1.9	13	100	0	50	48	0	16	36	1.46
63653844--63653883	19	2.1	20	86	9	57	15	10	12	62	1.54
63655732--63655888	42	3.7	42	74	6	140	17	22	15	43	1.87
63662168--63662318	42	3.6	41	79	3	158	16	21	17	44	1.87
63662203--63662262	21	2.8	22	72	7	61	13	18	16	51	1.76
63668349--63668420	35	2.1	35	84	5	92	44	8	16	30	1.77
63671666--63671752	11	7.8	11	73	14	54	68	2	6	21	1.24

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   205   206   207   208   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226