genome.fa.s9.2.7.7.80.10.50.1000.49.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  49  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)
20280026--20280061	2	18.0	2	100	0	72	50	0	0	50	1.00
20280065--20280149	3	27.3	3	75	15	75	60	3	2	34	1.27
20280035--20280149	14	9.8	11	75	19	60	57	2	2	37	1.26
20280128--20280165	14	2.6	15	88	12	53	63	0	2	34	1.09
20280686--20280737	21	2.4	21	84	12	70	78	7	9	3	1.06
20284104--20284223	50	2.4	50	79	5	136	29	24	25	20	1.99
20290488--20290530	15	2.9	15	79	3	52	58	2	0	39	1.11
20290668--20290702	19	1.9	17	88	11	52	40	0	2	57	1.14
20290831--20290886	21	2.7	21	70	10	51	33	26	17	21	1.96
20291630--20291706	28	2.8	27	79	11	77	31	1	3	63	1.20
20291700--20291751	20	2.7	20	72	3	52	44	0	1	53	1.11
20291869--20291908	20	2.0	21	85	5	55	32	0	5	62	1.17
20298032--20298073	22	1.9	22	95	0	75	28	4	14	52	1.62
20303652--20303808	2	78.5	2	100	0	314	50	0	0	49	1.00
20303876--20303903	2	14.0	2	100	0	56	50	0	0	50	1.00
20303938--20303981	2	22.0	2	100	0	88	50	0	0	50	1.00
20304110--20304211	41	2.5	41	91	0	168	30	26	21	21	1.98
20314963--20315002	20	2.0	20	85	0	53	45	5	5	45	1.47
20324312--20324336	11	2.3	11	100	0	50	48	16	24	12	1.79
20327638--20327701	22	2.9	22	95	2	110	32	3	1	62	1.20
20331451--20331479	9	3.0	10	90	10	51	20	0	0	79	0.74
20331451--20331479	5	6.0	5	92	8	51	20	0	0	79	0.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20333805--20333948	49	2.9	49	90	1	207	24	15	29	31	1.95
20337143--20337560	46	9.6	45	84	11	527	34	14	22	28	1.93
20337271--20337425	36	4.0	36	79	15	184	36	14	20	28	1.92
20337225--20337560	82	4.0	81	87	7	460	34	15	22	28	1.94
20337179--20337560	128	3.0	126	81	12	478	34	14	22	28	1.94
20340344--20340443	29	3.4	29	79	4	94	31	27	5	37	1.78
20340912--20341024	3	37.0	3	77	13	90	72	0	27	0	0.85
20340916--20341041	26	5.0	25	75	16	109	74	0	25	0	0.82
20340912--20341034	42	2.8	42	82	7	149	73	0	26	0	0.84
20340913--20341055	6	22.3	6	77	14	92	74	0	25	0	0.82
20341477--20341520	5	8.4	5	83	14	54	20	0	2	77	0.88
20341477--20341519	16	2.6	17	76	23	56	20	0	2	76	0.89
20341466--20341514	22	2.3	21	83	13	64	22	0	4	73	1.00
20341825--20341857	14	2.2	15	89	10	50	27	9	12	51	1.69
20341899--20341962	21	3.1	21	77	2	67	42	14	9	34	1.77
20341917--20342104	18	10.4	18	69	13	66	35	12	9	42	1.75
20342007--20342161	53	2.9	53	80	7	161	36	11	10	41	1.76
20342066--20342095	15	1.9	16	93	6	53	36	10	13	40	1.78
20341958--20342158	18	11.3	17	72	13	122	34	11	10	43	1.76
20341940--20342157	17	12.3	18	74	14	141	33	12	10	43	1.77
20343582--20343606	7	3.6	7	100	0	50	28	0	0	72	0.86
20346943--20347029	43	2.0	43	100	0	174	34	13	21	29	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20358089--20358142	27	2.0	27	82	7	65	62	0	1	35	1.06
20363702--20363752	9	5.7	9	92	0	84	31	11	21	35	1.90
20363702--20363752	18	2.8	18	93	0	93	31	11	21	35	1.90
20374314--20374378	19	3.5	18	75	14	53	24	3	9	63	1.39
20381532--20381571	20	2.0	20	100	0	80	25	5	30	40	1.77
20381533--20381604	16	4.2	16	85	7	81	30	1	31	36	1.66
20381816--20381870	25	2.2	25	84	9	69	52	1	0	45	1.11
20383054--20383139	36	2.4	37	90	2	129	53	12	27	5	1.61
20385014--20385058	20	2.2	21	88	4	65	24	2	2	71	1.09
20397172--20397221	16	3.5	15	71	18	52	58	14	8	20	1.61
20401339--20401386	15	3.3	15	85	5	55	37	14	2	45	1.57
20401352--20401392	15	2.7	15	88	0	55	31	17	0	51	1.46
20403313--20403380	18	3.8	17	73	11	55	47	25	1	26	1.61
20406834--20406876	22	2.0	22	100	0	86	37	13	25	23	1.92
20410786--20410869	42	2.0	42	100	0	168	30	21	9	38	1.85
20412250--20412325	26	2.9	26	78	0	89	39	25	17	18	1.91
20412508--20412642	27	5.0	28	82	6	136	19	17	21	41	1.90
20412508--20412651	54	2.6	54	85	3	173	19	17	20	42	1.89
20412525--20412651	27	4.7	27	84	5	157	18	16	22	43	1.88
20416541--20416574	13	2.5	14	90	4	52	50	0	5	44	1.26
20417586--20417645	12	5.1	12	78	9	70	31	1	1	65	1.13
20417586--20417645	6	10.2	6	74	15	54	31	1	1	65	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20417589--20417648	24	2.5	24	84	7	79	31	3	1	63	1.20
20417586--20417645	9	6.8	9	74	14	54	31	1	1	65	1.13
20417758--20417797	2	20.0	2	85	10	55	45	0	2	52	1.14
20417752--20417797	17	2.8	16	87	12	67	43	0	2	54	1.12
20417808--20417867	26	2.3	26	83	13	72	28	5	5	61	1.38
20417805--20417867	25	2.5	26	82	12	78	28	4	4	61	1.36
20427746--20427799	23	2.3	25	75	18	62	38	11	7	42	1.68
20434181--20434237	20	3.0	18	78	12	60	64	0	1	33	1.04
20434422--20434463	20	2.2	20	83	12	52	21	2	4	71	1.16
20434430--20434501	19	3.6	21	77	17	66	20	4	4	70	1.21
20434430--20434501	20	3.6	19	77	17	74	20	4	4	70	1.21
20436210--20436280	6	11.8	6	85	5	81	12	5	36	45	1.66
20436596--20436659	31	2.1	31	83	13	80	57	1	15	25	1.47
20437657--20437717	27	2.3	28	81	13	76	21	22	18	37	1.94
20442450--20442488	16	2.5	16	83	4	53	48	0	0	51	1.00
20448859--20448942	43	2.0	43	97	0	159	19	20	17	42	1.89
20450978--20451003	2	13.0	2	100	0	52	50	0	0	50	1.00
20451905--20451935	3	10.3	3	100	0	62	64	0	35	0	0.94
20452450--20452476	2	13.5	2	100	0	54	48	0	0	51	1.00
20459866--20459891	2	13.0	2	100	0	52	50	0	0	50	1.00
20461307--20461382	29	2.6	28	87	8	98	57	9	5	27	1.51
20463147--20463202	23	2.5	23	97	2	105	7	17	21	53	1.67
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20465922--20465960	19	2.1	19	85	0	51	12	17	2	66	1.35
20469157--20469209	6	8.8	6	100	0	106	33	0	16	49	1.47
20470733--20470810	40	2.0	40	82	5	95	24	21	1	52	1.54
20471712--20471760	19	2.6	19	96	0	89	59	22	0	18	1.38
20474302--20474662	90	4.1	93	82	13	439	49	9	9	31	1.67
20474520--20474662	75	1.9	75	95	0	259	49	9	9	31	1.67
20474961--20475012	17	3.1	17	85	0	77	38	7	1	51	1.42
20475408--20475469	19	3.2	19	76	13	72	51	14	14	19	1.76
20484215--20484280	29	2.2	30	84	7	82	43	1	6	48	1.36
20488467--20488494	2	14.0	2	100	0	56	50	50	0	0	1.00
20496283--20496330	20	2.4	19	80	13	60	31	4	0	64	1.12
20501702--20501737	19	1.9	19	94	5	65	63	2	11	22	1.39
20505347--20505399	17	3.0	18	75	13	56	45	1	0	52	1.11
20505347--20505397	18	2.9	18	77	13	61	45	1	0	52	1.12
20512486--20512519	15	2.2	16	89	5	52	50	26	0	23	1.50
20516590--20516662	3	24.3	3	94	0	128	63	0	2	34	1.09
20516661--20516726	3	22.0	3	100	0	132	33	0	33	33	1.58
20518539--20518565	3	9.0	3	100	0	54	33	33	0	33	1.58
20522870--20522915	17	2.8	18	84	15	64	28	41	30	0	1.56
20531976--20532037	17	3.5	17	75	12	61	24	8	8	59	1.53
20532200--20532241	19	2.2	18	87	8	57	16	19	9	54	1.69
20540537--20540694	43	3.7	42	74	7	122	33	25	16	24	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
20544913--20544965	27	2.0	27	85	3	72	52	11	16	18	1.73
20545542--20545598	29	2.0	29	89	0	87	29	12	26	31	1.92
20553723--20553761	20	2.0	20	89	0	60	51	10	0	38	1.36
20557042--20557101	29	2.1	29	100	0	120	28	33	8	30	1.86
20560819--20560871	2	26.0	2	96	3	97	49	0	1	49	1.12
20562043--20562080	12	3.0	13	85	14	53	36	2	0	60	1.11
20566703--20566754	25	2.1	25	96	0	95	40	13	19	26	1.88
20568484--20568518	18	1.9	18	88	11	54	8	11	22	57	1.61
20569113--20569147	18	2.0	18	88	5	54	20	5	2	71	1.19
20573492--20573532	16	2.6	16	88	0	64	41	14	4	39	1.67

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