genome.fa.s9.2.7.7.80.10.50.1000.85.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  85  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)
30337550--30337583	15	2.2	16	89	5	52	26	2	5	64	1.30
30339223--30339322	48	2.1	48	100	0	200	38	24	22	16	1.93
30341602--30341645	21	2.1	21	83	8	54	63	4	4	27	1.33
30341977--30342539	298	1.9	305	81	6	707	35	14	10	39	1.81
30345585--30345678	21	4.3	21	81	8	73	37	25	21	15	1.93
30345561--30345678	42	2.7	42	78	11	123	38	24	20	16	1.93
30345561--30345688	23	5.9	22	76	12	104	37	24	19	18	1.94
30346694--30346728	16	2.2	16	89	0	52	0	34	2	62	1.10
30352215--30352244	14	2.1	14	93	0	51	26	46	10	16	1.78
30353358--30353392	16	2.1	18	89	10	56	65	11	0	22	1.24
30353884--30353920	18	2.1	19	85	10	51	48	18	8	24	1.75
30357792--30357845	2	27.0	2	88	0	81	46	1	50	1	1.23
30359503--30359564	17	3.5	17	77	16	72	29	12	14	43	1.83
30359494--30359563	36	1.9	36	94	0	122	27	14	15	42	1.86
30364619--30364682	17	3.6	17	72	15	58	28	12	12	46	1.78
30364611--30364681	36	2.0	36	94	0	124	26	12	14	46	1.80
30364610--30364666	19	3.1	19	71	19	66	26	12	15	45	1.82
30364875--30364971	49	2.0	48	93	2	167	19	13	23	43	1.86
30365897--30365934	2	19.0	2	94	0	67	47	0	2	50	1.15
30366249--30366293	22	2.0	22	87	8	65	37	0	6	55	1.26
30366411--30366472	23	2.8	22	83	9	72	54	9	0	35	1.33
30366691--30366745	28	2.0	28	82	7	67	41	0	3	54	1.18
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30369304--30369440	40	3.5	40	80	8	163	19	19	22	37	1.94
30369329--30369389	20	3.0	20	82	0	86	13	19	26	40	1.88
30369273--30369389	20	5.8	20	76	0	81	17	22	23	36	1.95
30375487--30375552	31	2.1	31	88	0	96	46	10	10	31	1.72
30375647--30375699	9	6.1	8	81	14	61	32	1	1	64	1.15
30375647--30375703	17	3.2	18	87	5	71	31	1	1	64	1.13
30378096--30378155	26	2.3	26	85	2	86	40	21	21	16	1.92
30378096--30378164	26	2.7	25	82	6	84	39	20	23	17	1.92
30379663--30379723	26	2.3	27	82	2	79	55	11	18	14	1.68
30379853--30379895	6	7.3	6	97	2	79	48	0	13	37	1.43
30381784--30381869	15	5.7	15	83	1	100	32	17	2	47	1.60
30381802--30381869	30	2.3	30	97	0	127	27	17	2	51	1.60
30392902--30392956	25	2.2	25	83	6	67	23	21	16	38	1.93
30394709--30394749	20	2.0	20	95	0	73	24	7	19	48	1.74
30405763--30405921	27	5.9	27	75	7	126	23	16	19	40	1.90
30405777--30405925	54	2.8	54	80	2	156	21	17	18	42	1.89
30405777--30405925	81	1.8	81	84	5	203	21	17	18	42	1.89
30414461--30414668	40	5.2	40	79	2	195	29	22	18	29	1.97
30414461--30414641	79	2.3	80	81	0	211	28	22	18	30	1.97
30416859--30416892	17	2.0	17	100	0	68	41	0	11	47	1.40
30419613--30419638	11	2.4	11	100	0	52	34	0	7	57	1.27
30426185--30426283	23	4.3	23	93	0	162	20	21	27	31	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30431163--30431207	24	1.9	23	82	13	56	46	26	6	20	1.75
30432269--30432429	33	4.8	32	73	8	142	29	25	14	30	1.95
30432269--30432495	101	2.2	101	93	0	391	29	25	14	30	1.94
30432269--30432494	33	6.7	33	70	8	116	29	25	14	30	1.95
30438831--30438865	3	11.7	3	100	0	70	31	34	0	34	1.58
30440655--30440698	23	2.0	22	82	13	54	52	2	0	45	1.13
30440845--30440890	2	23.0	2	100	0	92	50	0	0	50	1.00
30445777--30445835	29	2.0	29	90	0	91	22	10	32	35	1.87
30446615--30446647	17	1.9	17	93	0	57	51	0	6	42	1.26
30457368--30457411	23	1.9	22	82	17	54	36	25	0	38	1.56
30457456--30457544	45	2.0	45	93	0	151	32	22	19	25	1.97
30457555--30457741	51	3.7	50	74	4	178	30	28	16	24	1.97
30464534--30464604	29	2.6	25	80	14	70	45	4	1	49	1.30
30470178--30470211	16	2.1	16	100	0	68	20	5	14	58	1.57
30471877--30471969	7	13.3	7	72	7	55	23	2	35	38	1.67
30471878--30471979	22	4.9	21	76	11	93	24	2	32	40	1.70
30471893--30471967	7	10.6	7	76	12	64	26	1	30	41	1.64
30477542--30477598	21	2.6	22	72	5	53	21	0	31	47	1.51
30478682--30478723	21	2.0	21	86	9	59	21	0	33	45	1.52
30485769--30485830	31	2.0	31	96	0	115	33	29	4	32	1.78
30493250--30493369	33	3.4	33	72	18	105	35	28	16	20	1.94
30493317--30493400	27	2.8	29	85	10	100	32	29	21	16	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30493275--30493473	102	2.0	102	90	0	317	32	27	18	21	1.97
30501020--30501047	3	9.3	3	100	0	56	32	0	0	67	0.91
30521990--30522046	29	2.0	29	89	0	87	40	0	5	54	1.23
30525290--30525329	21	1.9	21	84	0	53	42	0	0	57	0.98
30531592--30531663	29	2.4	29	81	4	81	25	12	15	47	1.80
30532861--30532888	7	4.0	7	100	0	56	57	0	0	42	0.99
30532908--30532973	27	2.4	28	87	2	98	42	0	3	54	1.15
30534706--30534753	22	2.2	22	92	0	78	35	12	22	29	1.91
30534948--30534979	17	1.9	16	93	6	55	37	9	0	53	1.34
30537439--30537516	20	4.0	20	75	8	79	38	20	32	8	1.84
30537893--30537965	25	2.9	25	89	6	103	54	0	2	42	1.14
30542960--30543032	25	2.7	27	77	12	71	53	4	2	39	1.34
30542978--30543026	25	2.0	25	88	8	73	55	2	2	40	1.23
30543090--30543147	8	7.1	8	74	21	50	37	0	0	62	0.96
30543090--30543129	17	2.3	18	87	12	57	37	0	0	62	0.95
30543096--30543147	24	2.2	24	85	0	68	36	0	0	63	0.95
30543506--30543536	14	2.3	14	94	5	55	70	0	0	29	0.87
30543560--30543611	21	2.5	20	80	20	61	67	3	1	26	1.18
30543559--30543622	15	4.3	15	75	13	53	67	3	1	28	1.15
30543560--30543619	23	2.6	24	82	12	74	66	3	1	28	1.17
30543580--30543630	15	3.4	15	81	5	59	70	1	0	27	0.98
30543567--30543632	23	2.8	24	82	15	77	68	3	1	27	1.13
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30545775--30545829	27	2.0	27	100	0	110	52	18	10	18	1.73
30547950--30548007	16	3.3	16	71	28	55	44	12	8	34	1.72
30551106--30551148	22	2.0	22	95	0	77	44	2	6	46	1.43
30551471--30551511	21	1.9	22	85	5	57	26	12	17	43	1.84
30557227--30557297	22	3.3	23	77	12	73	56	0	0	43	0.99
30557270--30557322	14	3.9	14	75	9	56	64	1	0	33	1.05
30557407--30557432	12	2.2	12	100	0	52	61	0	0	38	0.96
30557390--30557450	22	2.7	22	77	10	61	47	1	0	50	1.10
30559289--30559359	29	2.4	30	85	4	99	45	11	11	32	1.75
30563825--30564260	87	5.0	87	90	1	606	25	26	20	27	1.99
30564031--30564254	42	5.2	43	65	6	164	26	25	19	28	1.99
30581765--30581796	8	4.1	8	92	8	57	12	0	40	46	1.42
30581767--30581796	15	2.0	15	100	0	60	13	0	40	46	1.43
30581772--30581805	15	2.3	15	89	0	50	17	0	38	44	1.49
30582369--30582395	6	4.5	6	100	0	54	18	0	44	37	1.50
30582872--30582916	21	2.1	21	87	0	63	2	26	42	28	1.67
30583174--30583216	18	2.4	18	92	0	68	44	6	27	20	1.77
30584974--30584998	11	2.3	11	100	0	50	68	0	0	32	0.90
30585735--30585784	26	1.9	26	87	0	73	38	20	4	38	1.71
30585803--30585867	16	4.3	16	68	20	50	46	0	1	52	1.10
30585807--30585863	28	2.0	28	86	6	80	42	0	1	56	1.10
30585903--30585952	20	2.8	17	75	16	55	50	4	4	42	1.40
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30587546--30587576	16	1.9	16	93	0	53	70	9	9	9	1.33
30595193--30595219	6	4.5	6	100	0	54	14	0	85	0	0.61
30596480--30596560	41	1.9	43	87	5	121	38	18	18	24	1.93
30596971--30597193	49	4.6	46	76	8	178	24	23	17	34	1.96
30597677--30597808	46	2.8	46	82	4	158	30	20	25	23	1.99
30597677--30597820	47	3.1	47	84	4	175	31	20	25	22	1.98
30597677--30597854	46	3.7	48	80	7	157	29	17	25	26	1.98
30598052--30598109	21	2.7	21	75	5	62	29	8	1	60	1.36
30598295--30598538	48	5.0	48	79	6	251	22	22	20	34	1.97
30598295--30598487	98	2.0	93	81	8	219	22	22	22	33	1.98

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