genome.fa.s9.2.7.7.80.10.50.1000.21.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  21  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)
9549432--9549469	18	2.1	19	85	5	51	34	28	7	28	1.85
9551020--9551090	35	2.0	35	97	0	133	19	15	25	39	1.91
9557235--9557303	27	2.6	27	83	0	75	20	20	28	30	1.97
9575866--9576093	112	2.0	110	89	4	350	36	14	14	33	1.87
9579534--9579590	20	2.8	19	82	12	62	56	0	3	40	1.17
9579781--9579930	9	15.9	9	67	20	67	32	5	0	61	1.23
9580024--9580088	16	4.1	16	91	0	112	26	0	36	36	1.57
9580315--9580349	18	2.0	17	88	5	52	54	0	0	45	0.99
9580211--9580673	157	3.0	157	95	2	809	45	3	4	46	1.40
9580452--9580493	15	2.7	16	82	14	52	52	2	0	45	1.13
9580461--9580502	15	2.9	15	82	10	52	52	0	0	47	1.00
9580609--9580650	15	2.7	16	82	14	52	52	2	0	45	1.13
9580618--9580659	15	2.9	15	82	10	52	52	0	0	47	1.00
9584464--9584647	38	4.7	37	71	17	140	44	1	3	51	1.27
9584511--9584664	18	8.9	18	66	18	76	42	0	2	54	1.19
9584473--9584664	56	3.3	55	74	19	208	43	1	3	52	1.24
9584446--9584691	120	2.0	120	99	0	483	43	0	3	52	1.24
9584882--9584923	15	2.7	16	82	14	52	52	2	0	45	1.13
9584891--9584932	15	2.9	15	82	10	52	52	0	0	47	1.00
9592703--9592770	31	2.2	31	83	0	91	45	5	10	38	1.63
9593274--9593317	23	2.0	23	90	4	72	31	18	9	40	1.81
9595528--9595619	46	2.0	46	82	0	112	46	14	11	27	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9596773--9596807	2	17.5	2	100	0	70	51	0	0	48	1.00
9599512--9599862	183	1.9	183	89	0	549	24	24	19	31	1.98
9608894--9609018	64	2.0	64	86	0	178	22	20	24	33	1.97
9609535--9609592	11	5.5	11	75	19	52	31	0	1	67	1.01
9611463--9611520	25	2.4	23	81	10	71	27	25	10	36	1.89
9613703--9613783	25	3.3	25	77	13	87	30	23	24	20	1.99
9613780--9613832	24	2.2	24	82	0	70	43	20	18	16	1.88
9614400--9614441	21	2.0	21	85	0	57	40	21	4	33	1.74
9616788--9616852	29	2.3	29	82	12	89	60	1	7	30	1.34
9617275--9617312	2	18.5	2	84	15	51	44	0	5	50	1.24
9641948--9641986	2	19.0	2	89	5	60	51	0	2	46	1.14
9648705--9648738	2	17.0	2	100	0	68	50	0	0	50	1.00
9652414--9652470	28	2.0	28	81	18	66	28	8	1	61	1.36
9655721--9655800	39	2.1	39	81	9	92	56	2	2	38	1.26
9664828--9664885	28	2.1	28	90	6	91	60	12	12	15	1.59
9667240--9667349	57	1.9	57	90	3	177	30	20	24	23	1.98
9667481--9667676	67	2.9	67	96	0	356	20	17	33	28	1.96
9669812--9669837	4	6.5	4	100	0	52	50	23	0	26	1.50
9670826--9670883	18	3.4	18	88	6	77	29	8	24	37	1.85
9681474--9681524	13	3.9	13	77	10	59	39	21	3	35	1.72
9688627--9688651	4	6.2	4	100	0	50	72	0	0	28	0.86
9694576--9694639	32	2.0	32	85	11	87	37	9	9	43	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9695698--9695761	21	3.0	21	86	0	74	31	26	9	32	1.88
9699358--9699392	18	2.0	18	88	5	54	37	0	14	48	1.44
9701515--9701562	22	2.2	22	82	17	57	58	6	4	31	1.42
9708662--9708701	10	3.8	11	81	18	50	70	0	5	25	1.08
9709966--9710000	15	2.3	15	90	0	52	17	37	11	34	1.85
9711617--9711660	23	2.0	22	82	13	54	34	4	2	59	1.30
9714662--9714769	50	2.1	51	89	1	164	28	25	14	31	1.95
9725968--9726018	23	2.3	21	76	6	57	39	0	1	58	1.09
9730931--9730970	2	20.0	2	100	0	80	50	0	0	50	1.00
9736275--9736314	20	2.0	22	85	14	59	57	2	0	40	1.12
9740342--9740385	19	2.3	20	80	7	56	45	0	0	54	0.99
9747634--9747673	20	2.0	21	85	5	55	57	0	5	37	1.21
9747815--9747861	24	2.0	23	87	4	67	42	4	0	53	1.20
9747824--9747863	12	3.3	12	82	0	53	42	2	0	55	1.13
9747916--9747952	17	2.2	17	90	0	56	51	0	2	45	1.15
9747918--9748055	68	2.0	71	87	4	201	49	3	5	42	1.42
9750650--9750689	14	3.0	14	82	10	57	0	25	0	75	0.81
9750660--9750702	23	2.0	21	86	9	59	0	27	0	72	0.85
9750766--9750799	14	2.4	14	90	9	52	64	2	0	32	1.08
9750767--9750799	11	3.0	11	95	0	57	63	3	0	33	1.10
9751912--9751983	30	2.5	30	79	4	85	59	5	8	26	1.48
9754765--9754876	22	5.1	22	87	0	152	27	25	14	32	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9772151--9772181	15	2.1	15	100	0	62	35	19	0	45	1.51
9774425--9774451	11	2.5	11	100	0	54	22	7	18	51	1.70
9774856--9774890	18	2.0	17	88	5	52	45	0	0	54	0.99
9774695--9775003	157	2.0	155	94	2	548	46	5	3	44	1.42
9775123--9775161	16	2.4	16	86	0	51	28	33	2	35	1.71
9775135--9775176	16	2.6	16	92	0	66	30	35	0	33	1.58
9776969--9776994	2	13.0	2	100	0	52	50	0	0	50	1.00
9779039--9779067	2	14.5	2	100	0	58	51	0	0	48	1.00
9779067--9779099	2	16.5	2	93	0	57	54	0	45	0	0.99
9781486--9781590	52	2.0	52	100	0	210	25	7	15	51	1.69
9795953--9795984	3	10.7	3	100	0	64	0	31	0	68	0.90
9814805--9814843	17	2.3	17	86	8	53	79	2	0	17	0.84
9814802--9814835	15	2.3	15	90	10	52	79	2	0	17	0.86
9814802--9814835	8	4.6	7	86	13	50	79	2	0	17	0.86
9814761--9814843	9	9.6	9	70	20	52	69	1	1	27	1.03
9815126--9815151	13	2.0	13	100	0	52	38	7	23	30	1.83
9815167--9815248	39	2.1	39	86	4	112	23	4	3	68	1.25
9815158--9815277	10	12.5	10	71	9	72	26	3	2	67	1.19
9815177--9815276	39	2.5	39	80	7	105	28	4	2	66	1.21
9815159--9815279	9	12.8	9	73	12	73	27	3	2	66	1.19
9815253--9815302	9	5.8	9	79	9	50	34	0	2	64	1.05
9815254--9815304	17	3.0	16	73	21	50	31	0	1	66	1.03
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9815453--9815639	91	2.1	90	78	5	198	43	9	8	38	1.67
9819530--9819554	6	4.2	6	100	0	50	84	0	0	16	0.63
9820063--9820181	46	2.6	45	89	2	193	58	10	1	29	1.40
9832078--9832127	23	2.2	22	86	13	75	46	14	6	34	1.69
9838938--9838965	2	14.0	2	100	0	56	50	0	0	50	1.00
9841190--9841258	22	3.2	21	67	20	52	53	4	2	39	1.36
9845289--9845332	2	22.0	2	95	0	79	47	0	2	50	1.13
9855521--9855551	6	5.2	6	100	0	62	48	51	0	0	1.00
9856806--9856838	3	11.0	3	100	0	66	66	0	33	0	0.92
9858757--9858789	12	2.8	12	86	4	50	69	0	0	30	0.88
9861649--9861686	13	2.8	13	82	17	51	68	0	0	31	0.90
9868620--9868669	19	2.6	20	71	6	50	62	8	22	8	1.49
9871606--9871746	50	2.8	50	83	4	185	30	27	18	23	1.98
9871903--9871950	16	3.0	16	90	0	69	39	12	6	41	1.68
9879252--9879312	26	2.3	26	77	0	68	16	18	26	39	1.91
9879339--9879404	25	2.7	25	79	6	64	19	28	19	31	1.97
9885313--9885341	14	2.1	14	93	6	51	65	0	0	34	0.93
9889901--9889965	29	2.2	29	91	0	112	41	16	7	33	1.77
9897974--9898317	175	2.0	175	100	0	688	37	21	15	25	1.92
9898683--9898812	64	2.0	64	96	0	242	37	18	11	32	1.87
9903417--9903459	22	1.9	22	85	4	59	55	0	6	37	1.27
9904991--9905059	22	3.2	21	70	13	61	31	1	2	63	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9905007--9905031	13	1.9	13	100	0	50	24	0	4	72	1.02
9940741--9941227	29	16.7	29	84	8	614	27	3	27	41	1.71
9940925--9941227	81	3.6	79	88	5	315	27	2	28	41	1.69
9940838--9941227	110	3.4	109	86	6	474	27	3	27	41	1.71
9941210--9941249	7	5.6	7	82	5	53	12	0	40	47	1.41
9941615--9941649	18	1.9	18	94	0	61	34	8	31	25	1.86
9943705--9943788	29	3.1	29	69	22	92	42	0	26	30	1.55
9943715--9943822	22	4.6	22	72	20	78	40	0	30	28	1.57
9943678--9943799	51	2.4	51	94	0	217	44	0	26	28	1.60
9943777--9943818	21	2.0	22	90	4	68	45	0	35	19	1.50

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