genome.fa.s5.2.7.7.80.10.50.1000.40.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: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  64140413

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   

This is table  40  of  208  ( 24913 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)
11013182--11013229	24	2.0	24	87	0	69	18	12	18	50	1.78
11014598--11014632	8	4.2	8	85	7	52	71	8	5	14	1.29
11023901--11023944	19	2.3	19	84	4	52	52	0	9	38	1.33
11035317--11035452	60	2.3	60	80	2	139	29	33	13	22	1.93
11038422--11038510	25	3.6	25	77	8	83	41	12	13	32	1.82
11043301--11043335	18	2.0	18	94	5	63	11	31	45	11	1.76
11046987--11047055	22	3.1	22	93	0	111	30	17	26	26	1.97
11052888--11052935	18	2.7	17	81	15	53	43	0	14	41	1.45
11054208--11054443	86	2.7	86	87	3	314	30	23	17	28	1.97
11054208--11054443	43	5.5	43	82	5	280	30	23	17	28	1.97
11054208--11054462	130	2.0	129	85	5	345	31	24	16	27	1.97
11058535--11058560	12	2.2	12	100	0	52	23	26	7	42	1.81
11060281--11060511	9	26.1	9	73	11	131	31	0	19	48	1.55
11060281--11060384	43	2.4	43	93	0	181	32	0	17	49	1.53
11060312--11060462	61	2.5	61	93	2	252	29	1	19	49	1.57
11060312--11060485	61	2.6	68	81	15	238	30	1	19	48	1.56
11060583--11060636	21	2.7	20	85	5	65	48	1	3	46	1.30
11060597--11060636	21	1.9	21	94	0	71	47	0	5	47	1.24
11060618--11060708	34	2.6	36	87	5	123	57	0	2	40	1.11
11060725--11060821	21	4.5	21	77	12	90	47	1	12	39	1.48
11063067--11063191	29	4.4	29	73	17	109	41	4	5	48	1.45
11063129--11063156	14	2.0	14	100	0	56	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11063494--11063617	7	17.6	7	71	8	63	47	30	1	20	1.59
11063493--11063617	28	4.4	29	73	12	82	48	30	1	20	1.59
11063557--11063617	21	3.0	20	85	4	77	50	29	0	19	1.48
11063664--11063711	21	2.3	21	100	0	96	43	41	0	14	1.45
11063679--11063742	21	3.1	20	82	8	67	45	37	0	17	1.48
11068533--11068565	14	2.2	16	89	10	52	6	21	0	72	1.05
11072612--11072649	18	2.1	18	85	9	51	73	0	2	23	0.95
11076022--11076104	41	2.0	41	100	0	166	19	12	19	49	1.79
11078204--11078241	6	6.2	6	87	6	58	39	0	60	0	0.97
11078204--11078239	18	2.0	18	100	0	72	38	0	61	0	0.96
11078209--11078250	18	2.3	18	87	0	57	40	0	59	0	0.97
11078828--11078852	13	1.9	13	100	0	50	32	36	0	32	1.58
11081750--11081802	27	2.0	27	88	0	79	50	9	18	20	1.74
11088718--11088744	13	2.1	13	100	0	54	29	37	0	33	1.58
11090370--11090439	30	2.3	30	92	0	122	25	21	25	27	1.99
11090365--11090425	18	3.7	18	71	24	62	26	19	22	31	1.98
11090641--11090685	7	6.3	7	79	5	54	15	15	13	55	1.69
11090936--11091046	37	3.0	37	91	1	186	33	4	14	47	1.64
11090959--11091022	20	3.3	20	68	12	62	32	6	17	43	1.74
11091046--11091147	9	11.4	9	84	2	125	32	7	22	37	1.83
11097652--11097706	19	2.9	18	83	5	65	29	43	18	9	1.80
11097771--11097892	62	2.0	62	85	0	163	23	27	23	25	2.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11107113--11107190	37	2.1	36	83	6	95	30	25	8	34	1.87
11107523--11107566	21	2.0	21	83	12	54	34	22	15	27	1.95
11107783--11107823	19	2.2	18	87	12	57	36	4	12	46	1.63
11110789--11110842	17	3.3	16	78	12	56	3	11	5	79	1.02
11111908--11111964	18	3.4	17	80	7	62	35	5	1	57	1.31
11112006--11112085	24	3.6	23	77	12	71	36	3	2	57	1.30
11112342--11112753	109	3.8	109	91	0	637	30	15	18	34	1.93
11112342--11112766	219	1.9	217	88	1	645	30	16	18	34	1.93
11118173--11118229	24	2.4	24	85	5	80	28	38	21	12	1.89
11119909--11120250	43	8.0	43	84	3	395	35	23	14	26	1.93
11119909--11120250	126	2.7	127	80	3	382	35	23	14	26	1.93
11122663--11122707	23	2.0	23	100	0	90	51	0	35	13	1.41
11123072--11123121	20	2.5	20	87	6	75	14	2	6	78	1.03
11123520--11123559	14	2.8	14	80	3	53	35	45	0	20	1.51
11123707--11123759	22	2.5	21	90	3	79	62	0	1	35	1.06
11123707--11123777	21	3.3	20	79	15	72	60	0	1	38	1.06
11128154--11128196	2	21.5	2	100	0	86	48	0	0	51	1.00
11128196--11128220	4	6.2	4	100	0	50	0	0	24	76	0.80
11132289--11132337	20	2.5	20	90	6	73	12	4	6	77	1.09
11132732--11132780	15	3.3	15	82	5	64	32	42	4	20	1.71
11132776--11132830	28	2.0	28	85	0	74	49	25	0	25	1.51
11133224--11133350	40	3.2	40	81	0	137	25	22	17	34	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11133562--11133589	2	14.0	2	100	0	56	50	0	0	50	1.00
11139114--11139183	18	3.9	17	77	5	59	27	21	21	30	1.98
11139076--11139183	54	2.0	54	85	3	146	26	20	21	31	1.98
11146749--11146819	31	2.3	30	80	7	88	38	15	18	28	1.91
11146917--11146978	22	2.9	20	70	23	54	54	0	4	40	1.22
11147707--11147756	22	2.3	22	83	13	59	26	0	2	72	0.96
11147706--11147776	21	3.3	21	73	9	54	30	1	1	66	1.09
11148003--11148036	17	2.0	17	88	0	50	35	8	20	35	1.84
11148018--11148066	23	2.2	22	89	7	73	32	4	18	44	1.68
11156464--11156504	20	2.0	20	85	0	55	26	12	24	36	1.91
11159131--11159180	26	2.0	26	88	4	75	10	8	0	82	0.86
11160922--11161079	43	3.7	43	89	0	244	25	28	13	32	1.94
11161203--11161299	30	3.1	33	74	15	98	47	14	7	30	1.71
11165844--11165906	26	2.4	26	81	0	72	74	1	1	22	0.99
11165858--11165902	20	2.3	20	88	3	65	75	2	0	22	0.91
11165839--11165906	32	2.1	33	83	8	86	73	2	2	20	1.09
11165856--11165906	6	8.2	6	78	8	57	76	1	0	21	0.88
11168384--11168572	90	2.1	89	81	11	210	31	16	17	33	1.93
11168384--11168593	43	4.7	43	77	9	174	30	16	18	34	1.93
11170967--11171008	14	3.1	14	83	10	61	64	0	0	35	0.94
11172860--11172941	42	2.0	42	82	4	103	59	1	3	35	1.23
11173048--11173100	3	18.0	3	92	3	90	64	0	0	35	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11180729--11180811	37	2.2	37	91	4	132	32	12	12	43	1.79
11180739--11180815	37	2.1	37	97	0	145	33	11	11	42	1.78
11181033--11181084	20	2.6	21	77	20	65	65	1	1	30	1.14
11181031--11181087	19	2.8	21	79	10	66	63	1	1	33	1.15
11181033--11181094	19	3.1	19	73	15	54	61	1	3	33	1.22
11188278--11188344	34	2.0	34	87	0	98	20	20	7	50	1.72
11192885--11192933	18	2.8	18	76	14	57	34	0	0	65	0.93
11193977--11194049	29	2.5	29	75	4	76	32	5	1	60	1.28
11195379--11195414	18	2.0	18	88	0	54	36	2	0	61	1.11
11195388--11195452	33	2.0	33	87	0	94	36	3	0	60	1.13
11195296--11195452	43	3.5	43	81	7	181	35	3	1	59	1.24
11197960--11198008	24	2.1	23	81	11	55	57	0	6	36	1.24
11201312--11201365	21	2.6	21	77	8	65	31	27	7	33	1.84
11204170--11204228	22	2.5	24	72	25	63	42	8	20	28	1.81
11206131--11206174	18	2.6	16	83	13	61	68	2	18	11	1.30
11210617--11210661	23	2.0	23	91	8	76	33	0	2	64	1.06
11210728--11210906	68	2.9	59	83	13	250	44	9	5	40	1.60
11210817--11210844	9	3.1	9	100	0	56	57	10	0	32	1.33
11210758--11210928	68	2.5	68	96	1	310	46	8	4	39	1.56
11210917--11210958	16	2.6	16	92	0	66	42	7	2	47	1.43
11210758--11210950	68	3.0	66	91	6	274	47	8	4	39	1.54
11210932--11210993	23	2.7	23	82	2	72	48	1	1	48	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
11216446--11216494	23	2.0	25	88	7	75	67	4	0	28	1.09
11216454--11216492	18	2.2	18	90	0	60	69	2	0	28	1.02
11216686--11216730	22	2.0	23	91	4	74	20	8	8	62	1.51
11216690--11216741	23	2.2	23	79	3	59	23	7	7	61	1.49
11227862--11227955	31	3.0	31	92	3	161	31	8	14	44	1.76
11234096--11234191	31	3.1	31	93	3	165	31	8	13	46	1.73
11237180--11237364	43	4.3	43	80	4	133	29	15	23	31	1.96
11237209--11237386	43	4.2	43	78	8	186	28	14	25	32	1.94
11237285--11237376	42	2.2	43	82	3	116	31	14	23	30	1.94
11261695--11261846	81	1.8	84	80	6	186	32	31	7	28	1.84

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