genome.fa.s9.2.7.7.80.10.50.1000.173.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  173  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)
55300212--55300289	25	3.1	25	75	10	79	28	24	17	29	1.98
55300425--55300499	31	2.4	29	77	16	71	44	4	18	33	1.69
55304981--55305038	30	1.9	31	89	3	91	18	18	8	53	1.70
55307819--55308013	49	3.9	50	82	7	211	27	20	28	24	1.99
55317280--55317331	26	2.0	26	100	0	104	46	19	0	34	1.50
55334681--55334736	25	2.2	26	79	17	73	62	1	1	33	1.16
55335352--55335386	16	2.3	15	90	5	52	57	0	0	42	0.99
55343038--55343194	61	2.6	61	81	2	172	29	12	24	32	1.93
55343159--55343225	29	2.3	29	86	0	98	26	16	25	31	1.96
55345793--55345818	3	8.7	3	100	0	52	65	34	0	0	0.93
55350922--55350970	20	2.5	20	89	0	71	53	0	24	22	1.47
55367611--55367701	46	2.0	46	100	0	182	36	15	17	30	1.91
55375412--55375446	13	2.7	13	90	0	52	22	48	22	5	1.72
55377981--55378065	28	3.1	28	70	3	82	32	15	22	29	1.94
55401549--55401586	17	2.2	17	100	0	76	39	5	26	28	1.78
55404000--55404053	21	2.7	20	77	8	58	29	5	37	27	1.80
55406700--55406730	9	3.4	9	90	0	53	25	12	22	38	1.90
55406784--55406820	9	4.1	9	89	0	56	45	10	10	32	1.74
55406999--55407058	30	2.0	31	83	9	79	20	38	0	41	1.52
55407313--55407341	9	3.2	9	100	0	58	31	0	0	68	0.89
55410379--55410418	20	2.0	20	85	9	55	45	0	0	55	0.99
55412494--55412639	51	2.9	51	79	4	168	30	27	16	25	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55416999--55417024	2	13.0	2	100	0	52	50	0	0	50	1.00
55418811--55418835	6	4.2	6	100	0	50	32	0	0	68	0.90
55422904--55422991	43	2.0	43	88	0	131	47	14	12	25	1.79
55424834--55425071	29	8.2	29	77	4	183	25	14	23	36	1.93
55424834--55425071	58	4.1	58	77	4	203	25	14	23	36	1.93
55424964--55425027	30	2.2	29	85	2	83	26	17	20	35	1.94
55424884--55425071	88	2.1	87	81	2	216	25	15	23	35	1.94
55425951--55426099	41	3.6	41	97	0	280	20	29	21	28	1.98
55425952--55426127	41	4.3	41	89	2	255	22	27	20	29	1.99
55425954--55426127	82	2.1	82	91	2	287	22	27	20	29	1.98
55427543--55427567	13	1.9	13	100	0	50	40	24	4	32	1.73
55428674--55428734	30	2.0	30	83	0	77	21	32	31	14	1.93
55429750--55429792	18	2.4	18	84	7	61	23	0	4	72	1.04
55431422--55431461	21	1.9	21	94	0	71	42	12	7	37	1.71
55432993--55433067	20	3.8	20	87	0	96	10	25	37	26	1.89
55432991--55433066	40	1.9	40	91	0	125	9	25	38	27	1.86
55433713--55433795	22	3.8	22	77	13	73	19	3	2	74	1.07
55433753--55433798	19	2.4	19	85	7	58	13	6	2	78	1.04
55433714--55433795	34	2.4	34	80	8	87	19	3	2	74	1.08
55433753--55433803	18	2.7	19	85	8	61	13	7	1	76	1.09
55433828--55433874	22	2.1	22	84	7	60	23	4	4	68	1.26
55433837--55433875	12	3.4	12	82	13	55	25	2	5	66	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55436002--55436098	29	3.4	28	80	8	97	24	14	24	36	1.93
55436015--55436114	29	3.4	29	81	0	110	29	15	21	35	1.93
55439200--55439269	26	2.7	26	84	8	97	14	18	25	41	1.88
55439245--55439311	29	2.3	30	82	7	84	23	14	25	35	1.94
55439219--55439414	29	6.8	29	70	10	82	22	16	23	36	1.94
55441821--55441863	22	1.9	23	81	13	54	58	0	0	41	0.98
55442635--55442674	18	2.3	17	82	4	53	37	0	0	62	0.95
55442626--55442702	26	2.8	28	75	20	81	38	0	2	58	1.12
55457809--55457877	31	2.2	31	82	12	88	39	11	14	34	1.82
55459104--55459132	2	14.5	2	100	0	58	48	0	0	51	1.00
55461697--55461735	19	2.1	18	85	4	51	12	2	12	71	1.24
55465823--55465875	26	2.0	26	85	0	70	24	15	16	43	1.87
55472120--55472270	42	3.6	43	74	10	141	35	24	15	23	1.94
55472247--55472296	26	1.9	26	91	0	82	28	30	22	20	1.98
55472273--55472382	41	2.7	41	91	0	166	23	25	20	30	1.99
55475087--55475160	28	2.6	28	93	0	121	25	27	13	33	1.93
55475114--55475288	93	1.9	92	92	1	296	24	18	18	38	1.93
55478933--55478991	27	2.2	27	81	6	66	40	22	8	28	1.83
55478933--55478991	9	6.6	9	78	7	57	40	22	8	28	1.83
55478997--55479072	37	2.0	37	87	7	109	47	14	3	34	1.63
55479203--55479319	39	3.0	39	96	1	209	17	3	29	49	1.63
55479300--55479324	13	1.9	13	100	0	50	12	0	48	40	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55490766--55490827	24	2.5	25	73	2	63	24	20	19	35	1.96
55490965--55491016	26	2.0	26	81	7	61	40	7	17	34	1.78
55496264--55496481	107	2.0	107	100	0	436	28	23	12	35	1.92
55497858--55498118	61	4.3	61	75	3	204	35	14	23	26	1.94
55497858--55498086	122	1.9	122	81	3	282	33	15	24	27	1.95
55498154--55498219	29	2.3	30	78	7	73	33	16	24	25	1.96
55503028--55503548	261	2.0	261	96	0	954	30	14	17	37	1.90
55525282--55525324	21	2.0	22	81	4	52	20	4	11	62	1.46
55530102--55530189	42	2.1	41	97	2	167	34	27	13	25	1.93
55537209--55537252	24	2.0	24	82	13	58	43	13	4	38	1.65
55543790--55543841	24	2.2	24	89	0	77	34	3	7	53	1.48
55543790--55543853	24	2.7	24	85	4	67	34	4	10	50	1.59
55547161--55547217	24	2.4	24	87	0	78	36	5	8	49	1.57
55549646--55549695	24	2.1	23	85	10	66	52	2	2	44	1.24
55552823--55552909	38	2.2	41	80	13	103	62	2	4	31	1.28
55553079--55553158	19	4.2	19	75	13	76	27	2	5	65	1.27
55553090--55553140	9	5.4	9	79	6	57	31	0	3	64	1.11
55553076--55553146	29	2.5	28	80	11	81	29	1	5	63	1.26
55553076--55553158	28	3.0	27	76	15	80	27	2	4	65	1.26
55556085--55556171	42	2.1	42	84	0	111	28	19	31	20	1.97
55557080--55557130	17	3.0	17	94	0	84	33	13	13	39	1.84
55557813--55557897	21	3.9	23	80	11	108	36	24	22	16	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55557813--55557897	44	2.0	41	86	6	116	36	24	22	16	1.94
55559041--55559078	13	3.0	13	92	3	60	5	23	5	65	1.34
55559097--55559124	8	3.5	8	100	0	56	60	0	0	39	0.97
55560851--55560982	45	2.9	45	81	6	142	22	22	11	43	1.85
55566840--55566976	50	2.7	50	79	3	159	24	18	25	30	1.98
55566840--55566984	51	2.9	50	79	3	166	24	19	26	29	1.98
55568922--55568970	25	2.0	25	83	0	62	48	0	2	48	1.12
55576808--55577155	50	6.8	50	88	2	428	27	20	29	22	1.99
55593019--55593061	3	14.3	3	100	0	86	32	0	0	67	0.91
55593664--55593704	15	2.5	17	85	14	59	60	2	0	36	1.10
55593664--55593711	16	3.0	16	80	17	55	60	2	0	37	1.09
55594233--55594279	17	2.8	17	87	3	69	72	0	2	25	0.96
55594250--55594288	17	2.3	17	86	8	53	66	5	2	25	1.25
55603943--55604026	22	3.7	23	72	17	68	48	1	2	47	1.22
55604177--55604218	21	2.0	21	90	0	66	30	35	9	23	1.87
55604400--55604451	20	2.6	20	100	0	104	40	0	0	59	0.97
55604436--55604507	37	2.0	35	83	5	90	29	2	4	63	1.27
55622804--55623091	50	5.7	50	79	7	242	27	20	28	23	1.99
55622804--55623042	100	2.3	102	80	11	272	25	20	30	23	1.99
55630422--55630669	50	4.8	50	81	3	244	25	19	31	23	1.98
55630422--55630670	100	2.4	102	82	5	279	25	19	31	23	1.98
55630589--55630708	50	2.4	49	80	6	136	30	19	26	23	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
55630918--55630949	12	2.7	12	95	0	55	56	6	18	18	1.62
55631532--55631572	21	2.1	19	86	9	55	58	2	4	34	1.32
55634420--55634453	14	2.4	14	100	0	68	0	8	23	67	1.18
55649447--55649502	25	2.2	26	84	12	71	67	3	25	3	1.22
55662203--55662227	13	1.9	13	100	0	50	36	8	8	48	1.62
55662324--55662435	25	4.5	25	81	7	86	21	21	23	33	1.97
55678645--55678678	14	2.5	14	95	4	61	14	0	35	50	1.44
55681916--55681967	17	3.1	17	81	13	54	59	3	1	34	1.27
55681926--55681972	25	1.9	24	86	4	67	63	4	0	31	1.13
55681923--55681973	17	3.2	15	81	15	50	62	3	0	33	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   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