genome.fa.s8.2.7.7.80.10.50.1000.143.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   

This is table  143  of  190  ( 22705 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)
42138740--42138791	25	2.0	26	85	3	70	42	3	9	44	1.55
42145787--42145850	7	9.0	7	75	16	60	82	1	15	0	0.74
42145796--42145848	21	2.5	22	84	9	83	83	0	16	0	0.66
42147079--42148018	132	7.2	132	90	1	1367	28	17	23	30	1.97
42149468--42149534	3	22.3	3	93	0	116	29	0	2	67	1.06
42149533--42149600	3	22.7	3	100	0	136	0	0	32	67	0.91
42149999--42150051	2	27.0	2	96	3	99	49	0	0	50	1.00
42150374--42150404	15	2.1	15	93	0	53	19	9	6	64	1.45
42150450--42150770	109	3.0	109	92	1	522	32	15	17	34	1.92
42152112--42152156	8	5.1	9	79	15	58	48	0	0	51	1.00
42152113--42152156	18	2.5	17	89	7	70	50	0	0	50	1.00
42152113--42152159	9	5.5	8	82	12	58	48	0	0	51	1.00
42158595--42158657	21	3.1	21	72	19	62	60	1	4	33	1.27
42158609--42158681	30	2.5	29	82	12	87	58	1	4	35	1.25
42158649--42158697	18	2.6	19	83	6	73	59	2	4	34	1.28
42159825--42159862	20	1.9	20	89	10	60	28	0	21	50	1.49
42160739--42160790	24	2.2	24	85	0	68	25	21	13	40	1.89
42160772--42160817	24	1.9	24	86	0	65	28	15	17	39	1.90
42171498--42171527	2	15.0	2	100	0	60	50	0	0	50	1.00
42174868--42174946	32	2.4	32	89	2	113	15	35	25	24	1.94
42186751--42186790	20	2.0	20	90	0	62	32	17	25	25	1.97
42191246--42191287	18	2.4	17	84	11	50	30	23	16	28	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42192501--42192537	19	2.0	19	85	15	51	43	0	5	51	1.24
42192516--42192554	19	2.1	19	85	4	53	41	0	5	53	1.23
42194981--42195007	4	6.8	4	100	0	54	77	0	22	0	0.76
42198969--42199003	12	2.9	12	82	0	52	22	51	20	5	1.68
42199609--42199637	14	2.1	14	93	6	51	41	0	0	58	0.98
42201625--42201666	18	2.4	17	84	11	50	28	0	2	69	1.01
42213128--42213563	44	9.9	44	83	2	480	33	15	20	30	1.94
42215138--42215169	17	1.9	16	93	6	55	21	0	0	78	0.76
42215232--42215272	3	13.7	3	84	0	55	29	4	2	63	1.28
42215751--42215831	12	6.4	12	70	23	51	45	1	2	50	1.22
42215788--42215828	2	21.0	2	90	5	66	46	0	0	53	1.00
42215866--42215920	21	2.5	22	80	14	60	65	3	29	1	1.20
42216950--42216991	2	21.0	2	100	0	84	50	0	0	50	1.00
42222927--42222968	4	10.5	4	89	0	57	42	0	7	50	1.30
42222927--42222968	10	4.2	10	90	0	57	42	0	7	50	1.30
42222927--42222968	6	7.0	6	91	0	57	42	0	7	50	1.30
42225009--42225047	2	19.5	2	100	0	78	51	0	0	48	1.00
42226468--42226521	21	2.6	20	77	11	63	66	0	33	0	0.92
42226469--42226513	22	2.1	21	87	4	63	71	0	28	0	0.87
42229403--42229450	24	2.0	24	100	0	96	25	16	25	33	1.96
42230254--42230312	21	3.0	20	80	9	77	30	25	15	28	1.96
42234571--42234644	24	3.2	24	62	27	59	31	5	32	31	1.80
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42234569--42234754	46	4.0	46	95	0	309	33	8	27	30	1.86
42239551--42239599	21	2.6	18	84	12	62	67	2	2	28	1.13
42239997--42240102	48	2.2	48	86	0	140	21	9	39	29	1.85
42247341--42247379	6	6.5	6	100	0	78	33	48	0	17	1.48
42249751--42250193	126	3.5	126	87	1	629	30	17	22	29	1.97
42259941--42259982	21	2.0	21	90	0	66	45	0	14	40	1.45
42265699--42265792	25	3.8	25	79	8	93	30	15	30	22	1.95
42267132--42267196	32	2.0	32	100	0	130	32	18	30	18	1.95
42268804--42268850	22	2.2	22	85	14	64	55	2	0	42	1.12
42280492--42280530	21	1.9	21	89	5	62	25	48	15	10	1.76
42283431--42283785	42	8.3	42	90	4	493	30	21	22	25	1.98
42283431--42283785	85	4.2	85	91	3	520	30	21	22	25	1.98
42284219--42284263	21	2.1	21	83	0	54	2	42	24	31	1.67
42289823--42289956	25	5.4	23	74	13	83	35	3	21	39	1.71
42289814--42289954	34	4.2	34	68	15	114	35	3	21	39	1.71
42289814--42289855	18	2.5	16	88	7	57	38	2	21	38	1.67
42289888--42290304	9	47.2	9	76	11	305	34	2	15	47	1.59
42289882--42290003	59	2.1	59	90	3	192	38	0	20	40	1.58
42289922--42290065	25	5.8	25	73	18	81	36	0	18	45	1.54
42290141--42290177	14	2.7	14	95	4	67	35	8	0	56	1.29
42290485--42290545	23	2.6	24	84	10	81	59	1	6	32	1.33
42290521--42290821	34	9.1	34	74	21	291	52	3	9	34	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42290511--42290659	77	1.9	77	94	2	264	55	3	7	34	1.45
42290589--42290821	59	3.8	59	93	5	367	52	3	9	34	1.50
42290628--42290678	25	2.0	25	92	0	84	54	1	7	35	1.40
42290687--42290737	25	2.0	25	92	0	84	54	1	7	35	1.40
42292376--42292453	34	2.3	34	97	0	147	41	15	11	32	1.83
42292423--42292466	21	2.1	21	100	0	88	34	13	13	38	1.84
42293193--42293976	261	3.0	261	93	1	1319	34	20	17	27	1.95
42293838--42294076	115	2.1	115	91	0	388	32	19	18	29	1.96
42295258--42295402	75	1.9	77	84	2	195	30	24	25	19	1.98
42295501--42295698	72	2.8	71	79	6	213	28	24	22	24	2.00
42297697--42297737	17	2.4	18	80	8	50	39	0	12	48	1.41
42298241--42298303	32	1.9	33	90	3	101	42	3	0	53	1.16
42307188--42307222	17	2.1	17	89	10	54	82	2	0	14	0.77
42313565--42313614	19	2.4	21	78	21	61	26	0	4	70	1.05
42314652--42314678	2	13.5	2	100	0	54	51	0	0	48	1.00
42314744--42314822	17	4.3	18	74	13	72	62	1	2	34	1.17
42314745--42314816	20	3.8	20	76	7	62	61	1	2	34	1.19
42314851--42314913	19	3.3	19	81	2	63	60	1	0	38	1.07
42314743--42314913	9	18.6	9	69	20	81	60	1	1	35	1.17
42316396--42316439	20	2.3	20	84	7	56	59	2	2	36	1.23
42320224--42320438	21	10.3	21	78	5	204	15	21	17	46	1.84
42320223--42320421	42	4.7	42	80	4	231	16	21	16	46	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42322798--42322840	21	2.0	21	86	0	59	39	16	0	44	1.48
42326349--42326382	2	17.0	2	100	0	68	50	0	0	50	1.00
42329152--42329224	32	2.5	27	77	18	74	57	2	1	38	1.22
42332168--42332217	19	2.6	20	84	12	61	50	12	6	32	1.64
42345958--42346011	22	2.3	23	82	17	60	68	1	3	25	1.16
42346982--42347024	2	21.5	2	100	0	86	48	0	0	51	1.00
42357261--42357291	10	3.2	10	90	9	55	38	12	9	38	1.77
42364026--42364072	25	2.0	23	83	8	58	27	21	6	44	1.76
42367806--42367851	21	2.2	21	92	0	74	73	8	6	10	1.23
42369143--42369214	20	3.7	20	83	5	85	54	6	0	38	1.28
42381801--42381857	16	3.5	15	77	15	60	43	1	0	54	1.10
42381803--42381855	17	3.2	16	82	15	54	43	1	0	54	1.11
42383563--42383605	16	2.7	16	96	0	77	11	16	55	16	1.68
42384907--42385187	106	2.7	106	85	1	375	36	29	12	21	1.90
42389661--42389697	9	4.1	9	92	0	65	45	13	10	29	1.77
42390036--42390060	13	1.9	13	100	0	50	12	32	0	56	1.36
42398893--42399000	15	7.2	15	66	12	69	43	7	23	25	1.79
42398887--42399010	30	4.1	30	92	1	194	42	6	25	25	1.78
42400769--42400808	17	2.4	17	95	0	71	32	20	12	35	1.90
42402439--42402560	23	5.3	23	86	3	183	30	27	20	22	1.98
42402786--42402824	18	2.2	17	86	13	53	46	20	0	33	1.51
42408016--42408050	15	2.4	15	90	4	54	48	0	8	42	1.33
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
42410432--42410484	18	2.9	18	80	2	61	41	45	1	11	1.51
42410924--42410976	26	2.1	25	82	3	61	35	24	18	20	1.95
42413647--42413688	22	1.9	22	85	0	57	35	21	16	26	1.94
42414972--42415010	12	3.2	12	85	0	51	38	10	12	38	1.78
42414979--42415012	12	2.8	13	91	8	54	32	14	14	38	1.87
42416383--42416420	7	5.7	7	90	9	62	76	0	0	23	0.79
42416380--42416431	13	3.9	13	87	9	70	78	0	1	19	0.84
42416383--42416432	20	2.6	19	90	6	75	78	0	2	20	0.86
42416380--42416439	13	4.8	13	76	13	54	78	0	1	20	0.84
42420799--42420836	18	2.1	18	85	9	51	36	0	0	63	0.95

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