genome.fa.s9.2.7.7.80.10.50.1000.172.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  172  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)
54951426--54951529	52	2.0	53	84	1	138	28	25	23	23	1.99
54958852--54958896	23	1.9	23	82	13	56	20	4	28	46	1.69
54965731--54965769	20	2.0	19	90	5	60	58	15	10	15	1.62
54967906--54967987	27	3.0	26	81	10	78	25	17	20	36	1.94
54967942--54968026	27	3.1	27	89	0	134	20	16	22	41	1.90
54970250--54970308	25	2.3	27	82	5	68	45	15	1	37	1.56
54970274--54970335	27	2.3	26	88	5	88	33	14	3	48	1.60
54970251--54970436	26	6.9	26	70	21	84	37	17	2	41	1.64
54970368--54970452	13	6.5	13	77	1	89	36	21	2	40	1.66
54972701--54972753	4	13.2	4	80	7	63	45	24	0	30	1.54
54972716--54972762	25	1.9	24	91	4	76	42	23	2	31	1.66
54973799--54973852	27	2.0	27	88	0	81	33	20	18	27	1.96
54974310--54974340	11	2.8	11	95	0	53	12	9	22	54	1.67
54985157--54985194	16	2.4	16	86	8	51	31	2	5	60	1.33
54985164--54985204	17	2.4	18	84	15	61	34	0	4	60	1.18
54989951--54990080	26	4.8	26	67	21	88	44	4	13	37	1.64
54989948--54990120	84	2.1	84	98	0	337	42	3	13	39	1.62
54997003--54997043	19	2.2	19	86	8	57	43	4	0	51	1.23
55003397--55003764	185	2.0	185	91	1	594	28	13	16	41	1.87
55009765--55009987	45	5.0	45	83	1	272	28	15	22	33	1.95
55015104--55015321	45	4.9	45	85	1	269	26	15	24	33	1.95
55027041--55027222	90	2.0	90	98	0	355	39	15	6	39	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55033216--55033302	20	4.3	20	72	4	68	40	19	28	11	1.86
55033222--55033298	40	1.9	40	84	10	104	38	19	31	10	1.85
55040616--55040670	21	2.6	21	75	11	58	41	14	1	41	1.56
55041107--55041136	16	1.9	16	93	6	53	50	20	0	30	1.49
55043316--55043349	16	2.1	17	88	5	52	5	2	14	76	1.09
55055016--55055084	32	2.2	32	100	0	138	37	20	13	28	1.90
55056720--55056789	28	2.5	28	71	0	68	27	20	25	27	1.99
55057126--55057372	26	9.4	25	77	10	210	26	18	19	35	1.95
55057182--55057375	52	3.7	52	85	4	257	27	17	19	36	1.94
55057155--55057372	78	2.8	78	84	6	264	27	17	19	35	1.94
55065297--55065345	21	2.3	21	89	0	71	14	26	32	26	1.94
55069289--55069329	22	1.9	22	90	5	66	24	26	26	21	2.00
55071460--55071573	43	2.7	42	82	9	133	35	25	17	21	1.95
55072736--55072788	26	2.0	26	96	0	97	54	9	3	32	1.50
55076308--55076389	42	2.0	42	82	4	103	30	24	14	30	1.95
55079091--55079277	51	3.7	51	77	14	224	31	27	17	24	1.97
55079088--55079269	101	1.8	99	91	5	294	31	27	16	24	1.96
55083863--55083904	18	2.2	19	83	8	50	47	0	2	50	1.14
55083907--55083941	17	2.1	17	94	0	61	34	5	20	40	1.76
55089518--55089690	94	1.8	94	90	2	276	48	3	8	39	1.50
55089645--55089769	49	2.6	48	90	2	187	47	0	9	42	1.42
55091330--55091432	41	2.5	41	88	3	136	29	24	19	27	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55091287--55091432	41	3.6	41	82	3	125	27	25	19	27	1.99
55091836--55091880	2	22.5	2	100	0	90	48	0	0	51	1.00
55099967--55100008	12	3.5	12	81	12	50	9	42	26	21	1.83
55102213--55102333	49	2.4	49	79	6	129	30	19	26	23	1.98
55102544--55102592	20	2.5	20	81	15	66	57	6	22	14	1.59
55107951--55108002	17	3.1	16	72	10	50	50	0	1	48	1.12
55108027--55108065	16	2.5	15	83	8	51	43	0	2	53	1.14
55119677--55119943	103	2.6	104	93	1	446	20	19	29	29	1.97
55122118--55122147	13	2.3	13	94	0	51	30	6	6	56	1.51
55122542--55122580	17	2.3	17	90	0	60	17	7	2	71	1.21
55126564--55126605	9	4.8	9	85	8	52	66	2	0	30	1.04
55126592--55126636	21	2.2	20	84	8	54	62	0	0	37	0.96
55135172--55135233	30	2.1	30	93	3	108	32	9	0	58	1.31
55135883--55135931	17	2.9	16	85	8	62	30	0	2	67	1.02
55137619--55137663	17	2.6	17	86	10	56	55	4	0	40	1.20
55138171--55138225	24	2.3	24	84	6	67	36	5	5	52	1.48
55140157--55140208	24	2.2	24	89	0	77	34	3	7	53	1.48
55146507--55146609	19	5.3	19	63	13	57	14	33	18	33	1.91
55146496--55146624	39	3.3	39	87	3	188	16	32	19	31	1.94
55150681--55150724	23	1.9	23	95	0	79	40	20	9	29	1.83
55150681--55150730	23	2.2	23	88	0	73	42	20	10	28	1.84
55155882--55155961	26	3.0	27	81	3	83	17	18	23	40	1.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55156092--55156163	28	2.6	28	88	0	99	18	20	26	34	1.95
55156092--55156183	28	3.3	28	81	0	76	19	25	25	30	1.98
55162605--55162907	27	11.3	27	83	3	342	40	18	20	20	1.91
55163081--55163139	26	2.2	27	90	3	93	15	22	22	40	1.90
55163097--55163163	26	2.6	26	85	4	82	17	23	20	37	1.94
55163272--55163332	30	2.0	30	93	0	104	22	27	21	27	1.99
55163272--55163368	28	3.4	28	82	2	104	21	27	23	26	1.99
55171171--55171630	120	4.0	110	85	10	506	43	2	5	48	1.37
55171323--55171636	61	5.2	61	69	11	234	43	2	5	47	1.41
55171269--55171665	120	3.3	120	92	2	647	44	2	4	48	1.37
55171611--55171645	18	2.0	17	88	5	52	45	0	0	54	0.99
55171802--55171898	45	2.2	45	87	5	135	32	29	5	31	1.80
55171880--55171930	16	3.2	16	91	0	75	23	31	5	39	1.79
55176767--55176962	51	3.9	51	78	4	200	23	17	28	30	1.97
55176877--55176957	26	3.2	26	62	22	62	23	13	29	33	1.93
55176959--55177054	45	2.1	46	84	5	133	27	18	23	30	1.98
55179624--55179716	47	2.0	48	86	2	134	24	13	27	33	1.94
55192073--55192118	22	2.1	22	100	0	92	60	0	21	17	1.35
55196028--55196117	28	3.2	28	76	1	101	44	25	22	7	1.79
55196895--55196956	27	2.2	28	82	2	81	29	37	19	14	1.91
55203711--55203989	139	2.0	139	100	0	558	42	24	12	20	1.87
55205272--55205428	27	5.7	27	71	13	97	49	19	19	12	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55205352--55205448	28	3.5	28	80	1	97	46	22	20	10	1.81
55206150--55206211	26	2.3	28	76	15	69	22	32	19	25	1.97
55207989--55208143	57	2.7	57	86	1	195	43	8	18	29	1.79
55209644--55209683	18	2.2	18	100	0	80	20	20	17	42	1.89
55216785--55216832	24	2.0	24	83	0	60	39	4	8	47	1.53
55220177--55220207	6	5.2	6	96	0	53	0	16	19	64	1.29
55221049--55221100	24	2.2	24	89	0	77	36	3	9	50	1.54
55225721--55225761	20	2.0	20	100	0	82	36	4	19	39	1.73
55229499--55229579	43	1.9	42	92	2	135	34	14	2	48	1.58
55229587--55229668	17	5.1	17	72	14	75	31	2	4	60	1.30
55230228--55230264	18	2.1	18	94	0	65	32	8	10	48	1.67
55231730--55231947	28	7.6	28	75	11	140	43	22	15	17	1.87
55231733--55231985	30	8.7	30	77	8	179	43	24	15	17	1.87
55231730--55231985	88	3.0	88	89	5	355	43	23	15	17	1.87
55231730--55231955	58	3.9	56	76	8	197	42	23	15	18	1.88
55232308--55232458	56	2.8	54	85	4	212	22	28	15	33	1.95
55236023--55236102	22	3.6	22	86	0	115	27	15	26	31	1.95
55240288--55240658	105	3.6	104	93	1	611	19	20	29	30	1.97
55246412--55246564	22	7.0	22	90	0	225	26	26	14	32	1.94
55253195--55253565	105	3.6	104	93	3	597	19	20	29	30	1.97
55254859--55254916	26	2.3	24	79	8	62	67	1	1	29	1.11
55259761--55259796	18	2.0	18	100	0	72	55	11	16	16	1.68
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55261584--55261671	45	2.0	44	93	2	149	25	15	23	35	1.95
55269506--55269535	5	6.2	5	92	7	53	40	0	0	60	0.97
55270713--55270746	17	2.0	17	100	0	68	29	0	17	52	1.45
55275597--55275685	46	1.9	46	100	0	178	20	8	31	39	1.83
55277158--55277192	17	2.1	17	94	0	61	22	28	14	34	1.93
55277322--55277370	19	2.6	19	84	9	66	75	6	0	18	1.00
55278188--55278213	6	4.3	6	100	0	52	15	0	0	84	0.62
55279630--55279707	42	1.9	40	82	7	95	23	29	26	20	1.99
55289333--55289384	26	2.0	27	88	11	81	30	3	0	65	1.10
55292917--55292994	25	3.1	25	80	10	88	26	24	17	30	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   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