genome.fa.s6.2.7.7.80.10.50.1000.111.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: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  51074515

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   

This is table  111  of  168  ( 20060 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)
32674605--32674649	18	2.5	19	78	10	58	44	8	0	46	1.34
32675450--32675506	15	3.9	14	74	14	53	1	19	1	77	0.95
32676197--32676423	104	2.2	102	80	3	267	39	11	21	28	1.88
32682202--32682234	8	4.1	8	88	11	50	12	0	12	75	1.04
32684097--32684137	13	3.1	13	96	3	73	60	7	7	24	1.48
32685861--32685927	13	5.2	13	81	0	89	31	7	25	35	1.84
32691241--32691289	19	2.5	19	83	9	55	14	2	8	75	1.12
32704091--32704150	6	9.8	6	84	15	61	85	8	6	0	0.76
32704091--32704150	18	3.3	18	83	6	68	85	8	6	0	0.76
32704105--32704143	17	2.2	17	90	4	60	84	7	7	0	0.77
32704990--32705635	79	8.3	77	78	11	540	29	17	19	33	1.95
32705009--32705595	156	3.7	156	85	7	692	29	17	20	32	1.95
32705766--32705829	5	12.0	5	75	9	56	23	1	3	71	1.08
32705776--32705841	34	2.0	31	85	8	87	25	1	4	68	1.18
32706116--32706184	29	2.4	29	85	0	84	31	18	7	42	1.78
32706679--32706742	9	7.0	9	76	16	60	75	0	25	0	0.81
32706687--32706733	13	3.8	13	86	11	71	74	0	25	0	0.82
32706680--32706738	28	2.1	27	87	9	84	74	0	25	0	0.82
32707574--32707773	18	10.9	18	72	13	140	35	12	10	41	1.77
32707573--32707782	37	5.7	37	74	14	175	37	11	10	40	1.76
32707558--32707781	55	4.1	54	73	14	158	37	11	9	41	1.74
32711140--32711192	27	1.9	28	84	3	72	20	7	13	58	1.59
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32712409--32712448	16	2.5	16	83	0	53	40	25	10	25	1.86
32713688--32713715	2	14.0	2	100	0	56	50	0	0	50	1.00
32714872--32714896	3	8.3	3	100	0	50	36	32	32	0	1.58
32715278--32715339	30	2.0	31	84	9	83	33	14	9	41	1.79
32715376--32715404	15	1.9	15	100	0	58	34	13	10	41	1.79
32719420--32719465	19	2.4	19	92	3	74	39	8	6	45	1.61
32719429--32719473	19	2.4	19	96	0	81	35	6	4	53	1.47
32726790--32726825	17	2.1	17	94	0	63	41	19	13	25	1.88
32731273--32731304	2	16.0	2	100	0	64	50	0	0	50	1.00
32732654--32732683	13	2.3	13	94	0	51	6	10	16	66	1.41
32733525--32733601	5	15.6	5	75	21	65	38	0	3	57	1.17
32733553--32733601	19	2.5	19	90	9	73	42	0	0	57	0.99
32735175--32735216	6	6.8	6	86	2	57	16	21	16	45	1.86
32738105--32738211	38	2.8	39	76	13	123	40	3	5	50	1.44
32738185--32738233	22	2.3	22	76	16	57	40	2	6	51	1.38
32738466--32738501	16	2.2	16	95	0	63	22	30	5	41	1.76
32738546--32738705	80	2.0	80	97	0	302	36	6	7	49	1.58
32739271--32739305	15	2.3	15	90	0	52	65	0	0	34	0.93
32739323--32739368	22	2.1	22	91	0	74	32	17	10	39	1.84
32740259--32740340	30	2.6	32	77	11	89	30	18	4	46	1.70
32747118--32747157	20	2.0	20	100	0	80	5	20	10	65	1.42
32747508--32747534	3	9.0	3	100	0	54	0	33	0	66	0.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32752438--32752491	27	2.0	27	85	0	72	46	9	5	38	1.59
32754507--32754560	24	2.2	24	90	0	81	50	9	3	37	1.52
32757571--32757598	2	14.0	2	100	0	56	50	0	0	50	1.00
32760233--32760279	24	1.9	25	86	4	69	53	2	0	44	1.12
32762212--32762263	24	2.2	24	85	0	68	50	7	3	38	1.50
32764675--32764749	29	2.6	29	78	14	75	48	6	17	28	1.72
32766784--32766919	71	1.9	71	85	5	186	22	20	23	33	1.97
32768063--32768148	4	21.5	4	100	0	172	50	24	0	25	1.50
32772154--32772213	19	3.2	18	72	11	57	56	5	0	38	1.21
32776740--32776764	2	12.5	2	100	0	50	48	0	0	52	1.00
32776848--32776902	26	2.2	25	83	9	67	65	3	3	27	1.26
32777355--32777427	27	2.6	28	74	8	69	46	12	12	28	1.78
32777765--32777822	31	1.9	31	89	10	93	39	1	0	58	1.08
32778195--32778219	6	4.2	6	100	0	50	48	0	0	52	1.00
32778738--32778792	17	3.1	18	76	7	58	32	0	1	65	1.03
32780107--32780173	10	6.6	10	70	21	50	65	0	1	32	1.02
32780100--32780162	20	3.1	20	76	17	67	68	0	0	31	0.90
32780100--32780155	19	3.0	18	76	21	53	67	0	0	32	0.91
32784715--32784739	6	4.2	6	100	0	50	0	20	32	48	1.50
32797230--32797361	35	3.7	35	86	3	158	19	12	29	38	1.88
32800580--32800604	5	5.0	5	100	0	50	20	0	0	80	0.72
32805284--32805359	40	1.9	40	86	0	107	56	2	6	34	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32808176--32808264	40	2.2	40	80	4	99	24	28	24	22	2.00
32808428--32808492	23	2.9	22	78	21	64	24	30	1	43	1.64
32808427--32808492	11	5.9	11	73	19	57	24	30	1	43	1.63
32808452--32808551	51	2.0	51	86	4	139	27	27	2	44	1.65
32808560--32808589	14	2.1	14	100	0	60	26	0	0	73	0.84
32809692--32809717	7	3.7	7	100	0	52	26	0	15	57	1.38
32810990--32811424	22	20.0	22	83	3	490	46	27	0	25	1.58
32810989--32811425	43	10.1	42	84	6	473	46	27	0	25	1.58
32810990--32811424	65	6.7	64	84	5	525	46	27	0	25	1.58
32814607--32815128	126	4.2	125	86	3	726	31	22	15	31	1.95
32814607--32815175	252	2.3	250	87	1	800	31	22	15	30	1.95
32815289--32815322	9	3.8	9	92	0	59	58	26	0	14	1.36
32815289--32815324	18	2.0	18	100	0	72	55	27	0	16	1.42
32823241--32823302	23	2.5	25	78	19	67	17	6	6	69	1.32
32826880--32826997	51	2.3	51	79	4	123	40	7	19	32	1.80
32829762--32829824	27	2.4	27	86	2	83	42	4	0	52	1.22
32835096--32835136	20	2.0	20	90	0	64	51	0	4	43	1.23
32835820--32835854	18	2.0	17	88	5	52	45	5	0	48	1.26
32842587--32842629	20	2.2	20	92	8	72	44	18	0	37	1.50
32844933--32844977	19	2.4	19	85	7	56	33	17	8	40	1.81
32849016--32849073	24	2.4	24	88	0	89	32	10	25	31	1.89
32849365--32850121	100	7.6	100	88	0	1077	30	21	22	26	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32849365--32850121	199	3.8	200	87	1	1063	30	21	22	26	1.99
32849365--32850121	299	2.5	299	94	0	1316	30	21	22	26	1.99
32850136--32851092	127	7.3	128	81	8	1016	31	22	20	25	1.98
32850143--32850706	40	13.3	40	67	14	211	31	23	20	25	1.98
32850684--32850730	22	2.1	22	92	0	76	23	31	12	31	1.92
32850556--32850856	148	2.0	149	92	1	505	31	24	18	25	1.98
32850759--32851082	44	7.6	43	67	12	141	30	22	21	25	1.98
32850801--32850978	40	4.3	40	69	14	126	30	25	19	24	1.98
32852713--32852755	20	2.2	20	92	8	72	44	18	0	37	1.50
32854353--32854390	17	2.2	17	100	0	76	34	5	10	50	1.59
32854396--32854645	110	2.3	110	95	0	446	34	19	15	30	1.93
32854753--32854788	18	2.1	17	89	5	54	72	8	5	13	1.27
32855088--32855145	25	2.4	25	75	13	66	50	3	10	36	1.54
32855117--32855163	22	2.1	23	84	4	60	57	4	4	34	1.38
32857350--32857396	20	2.3	20	82	7	60	53	6	0	40	1.27
32857368--32857437	35	2.0	35	81	10	81	54	2	0	42	1.15
32861427--32861475	2	24.0	2	88	12	73	48	2	2	46	1.25
32861588--32861635	2	24.5	2	83	12	64	47	2	2	47	1.25
32862973--32863015	21	2.0	21	81	0	50	34	2	4	58	1.32
32865285--32865323	19	2.1	19	85	9	53	48	0	10	41	1.37
32868108--32868143	4	9.0	4	100	0	72	75	0	25	0	0.81
32870045--32870071	2	13.5	2	100	0	54	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
32873599--32873623	3	8.3	3	100	0	50	68	0	32	0	0.90
32884644--32884810	88	1.9	88	83	0	217	29	22	26	20	1.98
32885414--32885445	8	4.0	8	100	0	64	37	0	0	62	0.95
32886116--32886157	15	2.9	15	85	3	59	42	7	4	45	1.52
32891011--32891056	24	1.9	24	86	8	67	76	2	17	4	1.06
32894515--32894545	9	3.4	9	90	0	53	25	12	22	38	1.90
32894598--32894634	9	4.1	9	92	0	65	45	13	10	29	1.77
32894843--32894902	30	2.0	31	83	9	79	20	38	0	41	1.52
32908628--32908672	21	2.2	21	88	7	67	75	2	11	11	1.13
32908628--32908672	10	4.5	11	78	15	53	75	2	11	11	1.13

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