genome.fa.s9.2.7.7.80.10.50.1000.198.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  198  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)
62937610--62938337	22	33.0	22	81	6	789	46	28	0	25	1.57
62937618--62937671	27	2.0	27	88	0	81	38	38	1	20	1.63
62937639--62938337	43	16.0	44	82	5	789	46	28	0	25	1.57
62937639--62938337	65	10.7	65	82	5	784	46	28	0	25	1.57
62937789--62937853	29	2.2	29	86	10	89	46	30	0	23	1.53
62938285--62938339	21	2.3	26	67	29	66	49	25	0	25	1.51
62940306--62940997	124	5.5	124	88	4	951	29	22	16	30	1.96
62940306--62940997	250	2.8	251	89	1	1014	29	22	16	30	1.96
62942161--62942328	59	2.8	61	90	5	238	63	4	2	28	1.29
62942204--62942303	34	3.2	34	70	27	112	65	4	1	30	1.18
62942204--62942328	59	2.1	59	100	0	250	65	4	1	28	1.22
62942290--62942341	25	2.1	26	92	7	90	67	9	3	19	1.35
62942298--62942354	24	2.4	23	80	8	69	66	10	5	17	1.40
62942301--62942355	25	2.3	23	81	12	65	67	10	5	16	1.39
62943603--62943653	3	17.0	3	100	0	102	66	0	0	33	0.92
62945490--62945915	44	9.7	44	69	11	189	26	23	19	30	1.98
62945454--62945698	89	2.8	88	77	9	243	25	22	21	30	1.99
62945454--62945917	217	2.1	217	83	5	573	26	23	20	29	1.98
62945750--62945962	89	2.4	88	88	3	318	28	24	17	29	1.98
62946810--62946863	26	2.1	26	89	0	81	59	16	11	12	1.61
62958202--62958252	26	2.0	26	85	14	70	64	1	1	31	1.15
62962416--62962444	2	14.5	2	100	0	58	51	0	0	48	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
62963191--62963231	2	20.5	2	100	0	82	48	0	0	51	1.00
62963263--62963288	6	4.3	6	100	0	52	65	0	0	34	0.93
62965768--62965804	19	1.9	19	94	0	65	54	21	0	24	1.45
62966305--62966368	25	2.6	25	85	2	85	34	21	23	20	1.97
62966305--62966359	24	2.2	24	90	3	83	36	21	21	20	1.95
62972199--62972224	2	13.0	2	100	0	52	50	0	50	0	1.00
62972516--62972548	16	2.2	16	89	10	52	51	0	9	39	1.34
62972720--62972777	28	2.1	28	84	12	75	29	10	1	58	1.41
62974628--62974738	42	2.6	42	88	4	170	15	35	25	24	1.94
62974565--62974831	147	1.8	147	84	3	367	22	31	21	23	1.98
62974670--62974897	104	2.2	105	84	2	289	23	32	19	24	1.98
62983026--62983058	13	2.4	14	90	5	50	27	3	0	69	1.03
62986545--62986647	25	4.1	25	78	9	102	28	19	22	30	1.98
62997981--62998019	15	2.6	15	95	0	69	33	23	10	33	1.88
63007108--63007325	45	4.9	45	76	9	214	31	23	16	27	1.97
63007107--63007330	88	2.5	89	90	0	333	30	23	17	28	1.97
63012019--63012052	8	4.2	8	100	0	68	76	0	0	23	0.79
63013822--63013876	20	2.8	19	83	10	67	52	7	0	40	1.29
63014705--63014735	15	2.0	16	93	6	55	41	19	6	32	1.77
63017494--63017591	21	4.8	20	87	7	137	35	13	9	41	1.76
63017487--63017590	42	2.6	40	82	14	151	35	13	8	42	1.75
63017805--63017921	44	2.7	45	79	15	129	28	24	20	26	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
63018193--63020487	44	52.2	44	61	11	183	25	23	18	31	1.97
63018118--63020533	132	18.3	132	88	1	3519	25	23	18	31	1.98
63021682--63021733	22	2.4	22	87	9	72	0	17	0	82	0.66
63021673--63021720	15	3.0	16	87	6	62	0	22	2	75	0.91
63021683--63021727	15	2.9	15	81	15	56	0	20	0	80	0.72
63021695--63021730	19	1.9	19	94	5	65	0	16	0	83	0.65
63027039--63027081	3	14.3	3	80	9	52	67	2	0	30	1.03
63027039--63027105	33	2.0	33	83	11	84	68	2	1	26	1.12
63027302--63027340	19	2.0	21	85	10	55	69	5	10	15	1.34
63027542--63027596	19	2.8	19	88	5	83	38	9	10	41	1.72
63027883--63028090	42	4.9	42	88	2	265	27	27	17	27	1.98
63027644--63028090	43	10.4	42	79	4	286	27	27	17	27	1.97
63028428--63028487	21	2.9	21	89	0	84	5	45	15	35	1.68
63028433--63028498	21	3.1	21	88	0	78	6	43	16	33	1.73
63033724--63034008	9	32.8	9	72	14	224	31	2	21	45	1.63
63033713--63033817	25	4.2	25	81	11	124	33	2	20	43	1.66
63033729--63033979	34	7.3	35	75	14	179	31	1	21	45	1.63
63033757--63033981	43	5.5	43	70	19	117	31	1	21	46	1.60
63033832--63033870	19	2.1	19	85	9	53	30	0	17	51	1.46
63033728--63034008	25	10.8	25	76	14	193	30	2	20	45	1.63
63034082--63034136	16	3.7	16	69	18	55	34	1	18	45	1.60
63034084--63034153	28	2.5	28	88	2	104	35	2	17	44	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
63034331--63034480	53	2.8	53	94	0	255	44	4	10	40	1.58
63034393--63034504	13	8.5	13	76	5	100	44	3	10	41	1.56
63034393--63034531	66	2.1	66	82	0	161	44	2	10	41	1.54
63034982--63035479	229	2.2	227	82	3	572	31	17	23	26	1.97
63034963--63035479	114	4.5	112	79	6	511	31	18	23	26	1.97
63037256--63037323	21	3.3	21	85	4	93	35	20	42	1	1.61
63037771--63037978	42	4.9	42	84	7	196	24	23	21	31	1.98
63037795--63037979	85	2.2	84	85	8	250	22	22	22	32	1.98
63037795--63037999	43	4.8	42	85	5	252	22	22	22	31	1.98
63039305--63039335	9	3.4	9	90	0	53	25	12	22	38	1.90
63039388--63039424	9	4.1	9	92	0	65	45	13	10	29	1.77
63041809--63042071	83	3.2	82	78	11	252	35	20	15	28	1.94
63043501--63043700	108	1.9	106	87	2	292	37	18	16	29	1.92
63046113--63046212	44	2.3	44	79	10	107	32	24	13	31	1.93
63046202--63046365	44	3.7	44	85	1	204	22	24	22	30	1.99
63046813--63047028	87	2.5	87	93	1	362	24	23	23	29	1.99
63047035--63047583	44	12.6	43	68	11	205	28	24	19	28	1.98
63047028--63047583	218	2.6	218	90	1	873	28	24	19	28	1.98
63047588--63047762	50	3.5	50	72	6	140	28	17	19	34	1.95
63047582--63047773	100	1.9	99	84	1	258	29	18	19	32	1.96
63056486--63056526	21	1.9	22	85	5	57	17	31	2	48	1.60
63059300--63059493	108	1.8	106	89	2	307	35	19	17	27	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
63061785--63062145	41	8.8	41	83	3	431	28	26	21	23	1.99
63063396--63063478	43	1.9	43	82	4	105	20	19	27	32	1.97
63063405--63063509	43	2.4	43	73	9	97	23	20	27	28	1.99
63066454--63066487	16	2.1	17	88	5	52	47	0	8	44	1.34
63083277--63083534	45	5.7	45	71	12	179	30	19	23	25	1.98
63083458--63083941	181	2.7	180	84	4	591	32	20	19	27	1.97
63083696--63083791	44	2.2	44	79	3	104	33	18	20	27	1.96
63083825--63083995	89	1.9	89	82	4	211	30	20	22	26	1.98
63084291--63085501	605	2.0	605	89	1	1874	31	19	17	30	1.96
63085992--63086070	22	3.5	22	79	11	81	34	7	2	55	1.42
63086063--63086146	41	2.0	41	95	0	150	34	1	5	58	1.30
63086352--63086383	15	2.1	16	94	5	57	31	3	0	65	1.08
63087992--63088078	43	2.0	43	100	0	174	27	20	20	31	1.98
63090240--63090358	42	2.8	43	75	3	125	31	23	16	27	1.96
63094528--63094700	91	1.9	90	86	8	244	36	15	11	36	1.83
63094611--63094933	77	4.1	78	80	5	366	34	15	11	38	1.84
63094611--63094933	158	2.1	155	84	3	407	34	15	11	38	1.84
63094930--63095175	85	2.9	84	83	5	302	31	10	11	46	1.73
63105014--63105064	20	2.5	20	100	0	102	64	0	35	0	0.94
63105124--63105156	15	2.1	16	88	5	50	81	0	12	6	0.85
63105317--63105395	34	2.3	35	82	6	90	64	2	6	26	1.30
63105352--63107185	159	11.6	160	90	3	2673	53	9	8	28	1.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
63105352--63107185	320	5.8	316	88	5	2609	53	9	8	28	1.62
63109388--63109435	8	6.1	8	92	4	80	50	27	0	22	1.50
63109457--63109498	8	5.4	8	80	5	50	50	23	0	26	1.50
63109699--63110063	183	2.0	183	95	0	649	29	24	23	22	1.99
63111487--63111549	29	2.2	29	94	0	108	28	25	12	33	1.92
63113138--63113166	3	9.7	3	100	0	58	34	0	0	65	0.93
63115522--63115588	3	22.3	3	100	0	134	67	0	0	32	0.91
63115567--63115787	76	2.8	77	73	11	198	49	10	5	34	1.60
63115567--63115658	40	2.4	37	80	15	107	53	8	4	33	1.52
63115984--63116014	14	2.3	13	94	5	53	6	32	0	61	1.21

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