genome.fa.s9.2.7.7.80.10.50.1000.27.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  27  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)
12225811--12225920	53	2.1	53	86	6	152	34	1	6	57	1.35
12230388--12230413	3	8.7	3	100	0	52	34	0	30	34	1.58
12236017--12236065	3	16.7	3	93	4	82	36	0	0	63	0.95
12236249--12236291	13	3.2	13	87	9	52	74	2	6	16	1.14
12237334--12237421	23	4.0	23	77	7	92	18	19	20	42	1.90
12239118--12239170	27	2.0	27	85	7	72	58	1	1	37	1.20
12243759--12243869	22	5.0	22	87	0	150	31	14	26	27	1.95
12246355--12246381	3	9.0	3	100	0	54	66	0	0	33	0.92
12246636--12246680	4	11.2	4	80	0	54	42	0	0	57	0.98
12246637--12246680	8	5.5	8	97	0	79	40	0	0	59	0.98
12254311--12254375	31	2.1	31	94	0	112	27	16	10	44	1.81
12258834--12258864	7	4.4	7	100	0	62	25	16	0	58	1.38
12268570--12268632	23	2.7	23	80	9	58	61	3	1	33	1.21
12268586--12268632	22	2.1	23	84	4	60	61	4	2	31	1.27
12269389--12269443	3	18.3	3	92	0	92	69	1	0	29	0.99
12269442--12269476	3	11.7	3	93	0	61	31	0	2	65	1.07
12270039--12270093	22	2.5	22	80	19	69	43	1	30	23	1.64
12270039--12270092	11	4.8	12	80	15	62	42	1	31	24	1.65
12271553--12271603	20	2.5	20	78	6	50	54	1	3	39	1.30
12280060--12280099	9	4.3	9	84	6	53	17	5	0	77	0.94
12284151--12284184	13	2.6	13	90	9	52	73	8	8	8	1.25
12284627--12284656	14	2.1	14	93	0	51	36	10	43	10	1.72
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12284668--12284732	33	2.0	33	90	6	105	40	3	43	13	1.60
12286488--12286695	114	1.8	113	87	4	312	41	8	7	42	1.62
12287696--12287755	31	1.9	31	89	0	93	48	15	8	28	1.73
12297477--12297512	16	2.1	16	90	10	54	27	0	8	63	1.23
12297535--12297580	22	2.0	22	83	8	56	36	2	2	58	1.22
12297551--12297595	23	2.0	22	82	4	54	40	4	2	53	1.33
12297656--12297698	17	2.5	17	84	3	50	30	0	2	67	1.03
12297869--12297910	18	2.3	18	80	8	50	61	9	2	26	1.39
12305990--12306047	5	11.2	5	89	7	80	36	0	3	60	1.14
12306048--12306080	15	2.1	16	94	5	59	81	0	6	12	0.85
12306757--12306821	3	21.7	3	80	0	76	35	0	3	61	1.12
12306757--12306821	27	2.4	27	100	0	130	35	0	3	61	1.12
12309022--12309119	42	2.3	42	87	3	135	21	30	12	35	1.90
12324074--12324285	45	5.0	39	78	15	183	19	19	21	39	1.92
12324101--12324300	45	4.4	45	91	0	310	19	19	21	40	1.92
12325186--12325210	11	2.3	11	100	0	50	24	8	28	40	1.83
12335011--12335213	21	9.7	21	67	4	113	42	17	23	16	1.89
12334994--12335198	42	4.9	42	88	0	275	41	17	24	17	1.89
12335298--12335369	24	3.0	24	89	0	108	19	25	9	45	1.80
12344458--12344495	19	2.0	19	85	10	51	52	0	0	47	1.00
12344458--12344550	29	3.0	30	75	7	89	45	0	3	51	1.17
12348310--12348338	2	14.5	2	100	0	58	48	0	0	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12350959--12351145	25	7.8	25	80	9	180	22	21	17	37	1.94
12351073--12351135	22	2.9	20	81	11	56	17	26	19	36	1.94
12358247--12358280	17	1.9	18	88	5	52	35	26	0	38	1.57
12360525--12360553	15	1.9	15	100	0	58	41	20	0	37	1.53
12375682--12375738	28	2.0	28	100	0	114	33	17	3	45	1.65
12379543--12379650	22	4.9	22	87	0	144	31	14	26	26	1.95
12393554--12393617	26	2.5	26	76	16	71	45	4	1	48	1.32
12393624--12393677	20	2.7	19	77	2	54	31	3	0	64	1.11
12393679--12393715	15	2.5	15	90	0	56	29	5	2	62	1.31
12401767--12401793	14	1.9	14	100	0	54	29	22	11	37	1.89
12418139--12418183	22	2.0	22	86	0	63	51	13	13	22	1.75
12420187--12420216	2	15.5	2	93	6	53	50	0	0	50	1.00
12426122--12426150	3	9.7	3	100	0	58	68	0	0	31	0.89
12434710--12434761	23	2.2	24	83	10	63	48	1	3	46	1.31
12434758--12434805	21	2.2	23	85	7	64	54	0	4	41	1.20
12443743--12443800	9	6.4	9	85	0	71	41	24	6	27	1.80
12443743--12443800	27	2.1	27	87	0	80	41	24	6	27	1.80
12443902--12443936	13	2.7	13	90	0	61	11	0	45	42	1.40
12443895--12443963	31	2.3	29	80	9	84	14	1	42	42	1.54
12446229--12446311	25	3.3	25	80	9	89	30	18	28	22	1.97
12446270--12446331	25	2.5	25	83	0	79	27	19	29	24	1.98
12446270--12446389	50	2.4	50	80	2	125	34	18	25	22	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12448607--12448670	20	3.2	20	78	14	78	64	1	4	29	1.23
12448587--12448738	39	3.9	39	73	13	125	63	1	5	29	1.27
12448559--12448679	30	4.0	30	72	6	84	61	0	4	33	1.23
12448586--12448742	11	16.2	10	66	21	68	62	1	5	30	1.28
12448922--12449002	10	8.3	10	69	13	53	29	4	1	64	1.22
12448922--12448993	19	3.7	19	75	10	74	30	5	1	62	1.26
12448921--12449022	29	3.5	29	75	12	102	32	5	0	60	1.27
12450479--12450513	2	17.5	2	100	0	70	48	0	0	51	1.00
12450745--12450808	22	3.0	21	78	19	53	26	1	0	71	0.94
12450745--12450809	4	15.2	4	78	15	51	27	1	0	70	0.96
12454774--12454884	56	2.0	56	87	8	165	55	1	0	41	1.16
12454761--12454884	56	2.2	56	85	11	164	54	1	1	41	1.19
12454884--12454931	25	1.9	25	91	0	78	58	0	2	39	1.10
12455488--12455537	25	2.0	25	92	0	82	42	0	2	56	1.11
12455535--12455695	26	6.0	28	69	22	96	37	3	0	58	1.18
12455543--12455680	23	5.5	23	67	19	71	37	2	0	58	1.18
12455514--12455581	22	3.0	21	73	16	57	44	0	1	54	1.09
12455535--12455695	27	6.0	29	71	17	93	37	3	0	58	1.18
12455543--12455695	52	2.9	49	79	11	171	37	3	0	58	1.19
12455630--12455695	10	6.4	10	70	13	53	36	3	0	60	1.12
12455638--12455689	22	2.5	20	82	14	54	38	3	0	57	1.17
12466459--12466515	26	2.2	27	84	6	73	66	7	0	26	1.17
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12466509--12466546	15	2.5	16	83	12	53	63	2	0	34	1.09
12471615--12471653	18	2.2	18	86	9	53	56	2	2	38	1.27
12497384--12497416	2	16.5	2	100	0	66	48	0	0	51	1.00
12501372--12501398	12	2.2	12	100	0	54	40	0	0	59	0.98
12501700--12501751	20	2.6	19	81	9	50	73	5	15	5	1.22
12502789--12502903	39	3.0	39	87	1	151	19	21	23	35	1.96
12511677--12511708	16	1.9	17	93	6	57	62	3	3	31	1.26
12511725--12511775	21	2.5	20	84	12	59	50	7	5	35	1.55
12511831--12511867	18	2.1	18	94	0	65	62	2	0	35	1.10
12511825--12511864	18	2.3	17	86	4	53	52	2	0	45	1.14
12514085--12514228	70	2.0	71	93	2	245	22	15	18	44	1.86
12514797--12514841	17	2.6	17	82	13	56	35	2	0	62	1.08
12516375--12516513	46	3.0	46	87	4	199	30	23	8	37	1.85
12517728--12517775	17	2.9	17	90	3	71	54	18	0	27	1.44
12517932--12517977	24	1.9	24	86	0	65	34	13	30	21	1.91
12518079--12518145	20	3.0	23	74	17	68	53	1	0	44	1.09
12524389--12524431	11	3.9	11	78	0	50	2	16	2	79	0.95
12528353--12528479	50	2.5	51	83	8	161	26	29	16	27	1.97
12530076--12530182	53	2.0	53	98	0	205	48	23	3	24	1.67
12531379--12531462	2	43.5	2	92	7	147	48	0	0	51	1.00
12541027--12541075	23	2.1	23	100	0	98	57	0	20	22	1.41
12555421--12555475	28	2.0	28	96	0	101	36	5	10	47	1.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12561496--12561528	2	16.5	2	100	0	66	48	0	0	51	1.00
12561687--12561728	21	2.0	21	81	9	50	11	9	11	66	1.44
12563889--12563974	39	2.2	39	97	0	163	34	4	24	36	1.76
12568320--12568368	22	2.2	22	86	13	66	65	0	4	30	1.11
12568551--12568591	21	2.0	21	85	0	55	43	0	4	51	1.23
12569240--12569279	20	2.0	20	90	0	62	55	7	0	37	1.29
12569293--12569336	22	2.0	23	86	4	63	63	2	2	31	1.19
12573056--12573099	2	22.0	2	95	0	79	52	47	0	0	1.00
12575357--12575575	113	1.9	114	98	0	422	33	16	19	30	1.94
12578584--12578644	22	2.8	21	75	9	59	60	1	1	36	1.16

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