genome.fa.s9.2.7.7.80.10.50.1000.23.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  23  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)
10493660--10493899	115	2.1	115	93	2	410	31	20	18	29	1.96
10494377--10494428	14	3.8	13	85	12	68	48	26	3	21	1.67
10494384--10494428	7	6.6	7	82	2	56	46	26	4	22	1.70
10494367--10494427	21	2.9	21	73	9	61	45	31	3	19	1.66
10494767--10494822	21	2.6	21	82	5	67	37	42	1	17	1.60
10495181--10495324	75	1.9	77	85	2	202	30	26	25	17	1.97
10495428--10495620	72	2.7	70	77	4	190	27	25	21	24	1.99
10507351--10507400	21	2.3	22	86	3	66	54	6	2	38	1.37
10513315--10513343	8	3.6	8	100	0	58	24	13	27	34	1.93
10516148--10516216	5	14.4	5	88	8	108	36	0	1	62	1.04
10516221--10516256	16	2.1	17	90	10	56	75	0	5	19	1.00
10530389--10530437	6	8.7	6	78	13	50	20	36	12	30	1.89
10530403--10530443	18	2.3	18	86	0	55	24	36	9	29	1.87
10537198--10537247	20	2.5	19	78	9	55	60	2	2	36	1.20
10537386--10537448	14	4.4	14	78	11	65	55	3	1	39	1.25
10537579--10537642	19	3.4	19	81	16	71	25	7	1	65	1.28
10537601--10537642	10	4.3	10	81	6	50	21	7	2	69	1.25
10538543--10538602	13	4.6	13	78	0	57	41	16	0	41	1.48
10538889--10538969	40	2.0	40	90	0	126	43	16	2	38	1.61
10541159--10541197	11	3.5	11	78	0	51	17	12	10	58	1.61
10541156--10541203	22	2.2	21	85	7	69	18	10	10	60	1.57
10546956--10547116	83	2.0	82	94	1	286	37	13	1	47	1.53
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10550142--10550166	3	8.3	3	100	0	50	68	0	0	32	0.90
10550663--10550688	6	4.3	6	100	0	52	46	0	53	0	1.00
10551833--10551899	35	1.9	35	93	0	116	43	8	20	26	1.82
10562291--10562365	23	3.3	23	94	3	134	32	26	21	20	1.97
10568449--10568482	18	2.0	17	88	11	52	50	11	0	38	1.39
10570456--10570484	2	14.5	2	100	0	58	0	48	0	51	1.00
10575788--10575818	16	1.9	16	93	0	53	12	0	29	58	1.35
10575825--10575880	10	5.4	10	75	12	51	19	0	3	76	0.93
10575915--10575947	15	2.2	15	89	10	50	33	24	6	36	1.80
10578392--10578471	37	2.1	38	86	2	108	22	18	22	36	1.95
10580299--10580359	28	2.2	28	100	0	122	70	0	19	9	1.15
10595055--10595448	153	2.6	152	91	3	623	29	7	7	55	1.55
10595370--10595405	8	4.2	8	86	13	54	27	2	0	69	1.02
10595764--10595802	19	2.1	18	85	4	51	25	0	7	66	1.18
10597121--10597160	17	2.4	17	78	0	53	37	0	0	62	0.95
10597122--10597156	16	2.1	17	89	5	54	34	0	0	65	0.93
10598733--10598779	23	2.0	24	88	8	71	34	2	0	63	1.06
10598746--10598794	23	2.1	24	85	11	66	38	2	0	59	1.09
10598957--10598989	15	2.1	17	88	11	52	27	6	0	66	1.15
10599414--10599457	20	2.2	20	83	0	52	18	4	31	45	1.69
10607227--10607294	23	3.0	23	93	0	118	44	1	7	47	1.40
10607230--10607308	13	6.5	13	72	16	62	43	1	8	46	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10610851--10610886	18	2.0	18	100	0	72	44	0	5	50	1.25
10627257--10627281	7	3.6	7	100	0	50	56	0	0	44	0.99
10628398--10628474	38	2.0	38	100	0	154	18	19	28	33	1.95
10628615--10628655	18	2.3	18	82	0	55	48	7	14	29	1.71
10636815--10636909	31	3.1	30	76	11	88	37	11	11	38	1.78
10650357--10650405	24	2.0	24	84	7	64	20	10	2	67	1.30
10655144--10655257	58	2.0	58	92	3	194	22	17	21	38	1.93
10665248--10665281	15	2.3	15	89	0	50	67	8	20	2	1.31
10665618--10665647	3	10.0	3	100	0	60	0	33	0	66	0.92
10671057--10671256	45	4.4	44	87	5	276	41	20	19	19	1.91
10671072--10671278	45	4.8	42	84	7	206	39	21	19	19	1.92
10671057--10671256	90	2.2	90	89	5	314	41	20	19	19	1.91
10674265--10674290	5	5.2	5	100	0	52	42	19	19	19	1.90
10675409--10675439	9	3.4	9	90	0	53	38	22	12	25	1.90
10676040--10676114	22	3.3	23	74	17	75	49	1	2	46	1.24
10676269--10676321	21	2.5	21	87	0	70	30	33	9	26	1.88
10677975--10678027	2	26.5	2	88	0	79	47	1	1	49	1.23
10688884--10688937	19	2.7	19	82	5	54	29	3	1	64	1.21
10691621--10691684	2	32.0	2	93	0	110	0	46	1	51	1.10
10699651--10699685	16	2.2	16	90	5	54	31	0	0	68	0.90
10708645--10708695	26	2.0	26	92	0	84	33	11	11	43	1.78
10712766--10712854	42	2.1	42	81	4	99	46	29	17	6	1.74
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10725167--10725195	14	2.0	15	93	6	51	13	34	17	34	1.89
10725900--10725943	14	3.1	14	93	0	70	25	15	25	34	1.95
10726132--10726174	19	2.2	20	84	12	54	53	4	4	37	1.43
10726145--10726193	20	2.7	19	79	14	50	63	4	2	30	1.24
10728001--10728046	20	2.2	21	84	3	67	67	0	4	28	1.10
10736917--10736941	2	12.5	2	100	0	50	48	0	0	52	1.00
10737191--10737239	21	2.3	20	80	19	55	30	2	8	59	1.38
10744427--10744464	2	18.5	2	84	15	51	47	0	5	47	1.24
10747292--10747361	34	2.1	34	83	5	88	34	4	0	61	1.16
10747419--10747478	31	1.9	31	93	6	104	55	8	1	35	1.40
10756379--10756480	50	2.0	50	94	3	179	45	24	6	23	1.77
10760755--10761023	137	1.9	139	90	3	436	47	13	13	26	1.79
10776949--10776977	8	3.8	8	95	4	51	0	6	0	93	0.36
10776946--10776976	15	2.1	15	94	5	55	0	9	0	90	0.46
10778608--10778638	16	2.0	16	93	6	55	41	0	6	51	1.27
10782519--10782562	18	2.4	18	85	7	63	63	4	0	31	1.14
10782546--10782589	18	2.4	19	80	7	54	70	2	2	25	1.10
10782747--10782798	25	2.0	26	85	3	70	55	1	3	38	1.29
10782747--10782801	26	2.1	26	83	6	67	54	1	3	40	1.28
10783411--10783443	14	2.4	14	90	5	50	3	27	0	69	1.03
10792734--10792767	16	2.1	17	88	5	52	67	2	0	29	1.05
10800685--10800729	20	2.3	20	80	3	56	68	0	31	0	0.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10801631--10801728	40	2.6	37	74	11	99	23	18	28	29	1.98
10805341--10805386	20	2.4	19	77	22	51	52	6	0	41	1.27
10816146--10816184	21	1.9	20	84	5	51	7	17	2	71	1.21
10828993--10829064	35	2.1	35	100	0	144	40	8	2	48	1.48
10840546--10840659	52	2.2	52	87	4	158	35	12	22	28	1.91
10840598--10840702	46	2.3	46	93	0	174	37	13	20	29	1.90
10840665--10840811	37	4.0	37	91	1	226	36	15	21	25	1.93
10845334--10845363	15	2.0	15	100	0	60	20	0	20	60	1.37
10846829--10846870	22	1.9	22	100	0	84	38	14	26	21	1.91
10848589--10848641	13	4.1	13	72	0	52	32	9	24	33	1.87
10848589--10848693	26	4.0	26	74	14	79	32	7	22	37	1.83
10848650--10848695	13	3.5	13	81	3	56	39	4	17	39	1.69
10853238--10853282	21	2.1	21	84	8	56	44	0	6	48	1.29
10870818--10870879	17	3.6	16	77	12	61	51	1	3	43	1.27
10870910--10870980	17	4.0	17	74	15	63	49	2	0	47	1.16
10870910--10870984	9	8.3	9	71	11	55	48	2	0	49	1.15
10870910--10870984	36	2.1	36	87	5	107	48	2	0	49	1.15
10870997--10871077	9	8.8	9	70	18	60	53	1	1	44	1.16
10871001--10871078	38	2.1	38	90	4	122	55	1	1	42	1.16
10870997--10871085	17	4.9	17	76	17	81	52	1	1	44	1.15
10871050--10871190	63	2.3	62	81	7	173	43	2	2	51	1.28
10871167--10871200	17	2.0	17	100	0	68	41	0	0	58	0.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10871184--10871236	27	1.9	28	84	3	72	45	0	3	50	1.19
10872714--10872779	33	2.0	33	88	8	98	71	1	3	24	1.09
10872754--10872778	13	1.9	13	100	0	50	80	0	0	20	0.72
10874571--10874616	23	2.0	24	87	12	69	34	13	4	47	1.62
10875575--10875613	17	2.3	17	86	0	51	33	2	2	61	1.23
10875603--10875696	22	4.3	23	75	15	78	44	1	3	51	1.24
10876479--10876506	3	9.3	3	100	0	56	32	32	0	35	1.58
10876504--10876530	12	2.2	12	100	0	54	18	40	0	40	1.51
10899021--10899068	24	2.0	24	95	0	87	52	16	14	16	1.76
10899023--10899074	24	2.2	24	89	0	77	53	21	11	13	1.70

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