genome.fa.s13.2.7.7.80.10.50.1000.133.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: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  58321163

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   

This is table  133  of  199  ( 23770 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)
40220456--40220492	20	1.9	19	89	10	58	24	32	0	43	1.55
40224056--40224093	19	2.0	19	100	0	76	31	21	10	36	1.87
40231320--40231348	14	2.0	15	93	6	51	27	0	3	68	1.05
40232076--40232277	49	4.1	50	87	5	252	30	17	19	33	1.95
40232239--40232306	29	2.3	29	94	0	118	26	19	22	32	1.97
40234284--40234326	23	1.9	23	90	4	70	37	4	18	39	1.72
40245415--40245465	23	2.2	23	89	6	77	29	9	19	41	1.84
40246450--40246483	17	1.9	17	88	5	50	44	11	14	29	1.81
40248234--40248266	10	3.3	10	87	12	50	48	27	0	24	1.51
40249239--40249271	4	8.2	4	93	0	57	24	3	0	72	0.98
40251039--40251095	22	2.6	22	85	0	78	36	21	29	12	1.90
40251475--40251525	28	1.9	27	84	11	70	31	13	1	52	1.51
40254096--40254140	21	2.1	22	87	4	65	40	2	2	55	1.24
40254090--40254139	18	2.5	20	79	17	59	38	2	2	58	1.21
40270070--40270118	24	2.0	24	100	0	98	24	24	16	34	1.95
40280457--40280486	2	15.0	2	100	0	60	50	0	50	0	1.00
40286827--40286941	42	2.7	43	81	4	135	23	17	27	31	1.97
40288852--40288891	21	2.0	21	90	5	64	35	32	0	32	1.58
40289491--40289639	30	5.0	30	85	0	199	36	17	14	32	1.90
40290036--40290139	9	11.4	9	85	6	129	24	10	25	39	1.87
40290298--40290323	12	2.2	12	100	0	52	15	26	34	23	1.94
40296839--40296889	20	2.5	20	75	12	50	29	25	13	31	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40298081--40298151	4	17.0	4	77	13	72	23	4	1	70	1.13
40298089--40298151	25	2.5	25	89	7	92	22	4	1	71	1.13
40298098--40298153	21	2.7	21	86	8	78	19	3	1	75	1.05
40298506--40298554	12	3.9	13	75	17	50	16	6	2	75	1.09
40302708--40302736	2	14.5	2	100	0	58	48	0	0	51	1.00
40305253--40305291	18	2.2	17	86	13	53	33	0	20	46	1.51
40305520--40305638	23	5.2	23	91	2	195	22	21	26	29	1.99
40306871--40306912	21	2.0	21	86	9	59	16	4	4	73	1.17
40306886--40306918	17	1.9	17	93	0	57	15	3	3	78	0.99
40307429--40307489	31	2.0	31	96	0	113	42	18	18	21	1.89
40309951--40310178	2	116.5	2	74	7	164	0	56	0	42	1.08
40314868--40315837	242	4.0	242	98	0	1852	32	13	22	31	1.93
40325106--40325448	114	3.0	114	97	0	643	32	12	23	31	1.92
40330816--40330853	13	3.0	12	88	11	58	63	2	0	34	1.09
40336289--40336484	98	2.0	98	90	0	311	29	15	20	34	1.94
40340332--40340407	29	2.5	30	78	4	82	50	10	3	35	1.56
40340328--40340407	31	2.7	29	78	5	88	50	11	3	35	1.56
40351039--40351077	20	2.0	20	84	0	51	64	0	0	35	0.94
40351642--40351710	29	2.4	29	97	0	129	47	11	7	33	1.67
40352254--40352286	16	1.9	17	88	11	50	60	0	0	39	0.97
40352224--40352299	27	2.8	26	80	17	84	53	1	2	42	1.23
40362440--40362473	13	2.7	13	95	4	61	50	0	11	38	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40363049--40363082	12	3.0	12	87	12	54	52	0	0	47	1.00
40363049--40363085	17	2.1	18	90	5	58	51	0	0	48	1.00
40365594--40365736	11	12.7	11	67	24	68	51	2	2	43	1.28
40365607--40365647	21	2.0	20	85	4	55	48	2	0	48	1.14
40365594--40365719	6	21.7	6	67	24	67	51	2	2	43	1.27
40365586--40365719	68	2.0	68	85	5	182	50	3	2	43	1.32
40365642--40365695	19	2.8	19	81	13	65	55	3	3	37	1.35
40366193--40366241	25	2.0	25	95	0	89	48	14	4	32	1.62
40367330--40367363	16	2.1	16	88	0	50	67	5	8	17	1.37
40378943--40378984	16	2.8	15	78	10	50	40	4	38	16	1.70
40384903--40384960	2	29.0	2	100	0	116	0	0	50	50	1.00
40385140--40385256	29	4.1	29	72	16	120	53	7	8	29	1.59
40387494--40387597	49	2.1	49	87	0	145	30	8	9	50	1.65
40388972--40389019	25	2.0	24	87	4	69	47	0	0	52	1.00
40388968--40389216	110	2.2	114	84	9	323	44	2	2	50	1.29
40389176--40389209	17	2.0	17	100	0	68	41	0	0	58	0.98
40389376--40389464	46	2.0	44	93	4	151	39	30	5	24	1.78
40389356--40389475	46	2.8	43	83	14	149	38	31	5	25	1.77
40400114--40400148	2	17.5	2	100	0	70	48	0	0	51	1.00
40400817--40400921	29	3.6	29	69	5	86	20	22	18	39	1.93
40403976--40404049	28	2.6	28	82	0	85	20	35	27	17	1.95
40407364--40407406	22	2.0	22	90	0	68	32	18	13	34	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40407459--40407503	19	2.4	19	92	0	72	24	6	31	37	1.81
40417286--40417311	5	5.2	5	100	0	52	42	19	19	19	1.90
40418063--40418121	30	2.0	29	83	6	73	42	0	37	20	1.52
40418336--40418372	9	4.1	9	92	0	65	29	10	13	45	1.77
40418425--40418455	9	3.4	9	90	0	53	38	22	12	25	1.90
40426229--40426275	25	1.9	25	82	4	60	51	17	4	27	1.64
40427060--40427087	2	14.0	2	100	0	56	50	0	0	50	1.00
40429501--40429597	51	1.9	50	83	8	124	32	12	8	46	1.71
40438311--40438349	2	19.5	2	94	0	69	48	0	2	48	1.15
40443060--40443101	16	2.7	16	85	10	52	85	4	9	0	0.72
40443063--40443101	18	2.2	17	86	4	51	87	2	10	0	0.65
40446989--40447027	20	2.0	19	90	5	60	43	7	15	33	1.75
40448380--40448460	20	4.1	20	74	6	74	8	28	19	43	1.81
40456078--40456166	38	2.4	38	82	1	99	33	19	15	31	1.93
40458268--40458319	26	2.0	26	85	7	70	36	30	9	23	1.87
40469415--40469479	29	2.2	29	83	5	78	44	18	7	29	1.77
40478487--40478545	29	2.0	29	93	0	100	27	8	16	47	1.76
40483462--40483952	51	9.7	50	81	7	498	29	26	15	28	1.96
40483462--40483952	102	4.9	102	88	5	626	29	26	15	28	1.96
40485955--40486004	25	2.0	25	100	0	100	44	8	8	40	1.63
40505704--40505962	138	1.9	138	81	7	316	31	10	6	52	1.59
40507831--40507884	19	2.8	19	82	0	81	38	14	9	37	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40508396--40508775	45	8.7	44	72	11	217	26	22	20	31	1.98
40508575--40508686	44	2.5	44	82	2	127	31	17	19	31	1.95
40508489--40508918	217	2.0	218	86	0	610	27	22	19	29	1.98
40509267--40509459	44	4.4	43	83	5	217	31	26	13	27	1.94
40509267--40509475	88	2.4	88	86	3	278	31	25	15	27	1.96
40509305--40509474	44	3.9	44	92	0	277	31	25	15	26	1.96
40510721--40510798	6	12.8	6	90	5	122	1	17	0	80	0.77
40515625--40515660	2	18.5	2	88	5	56	50	2	0	47	1.15
40515625--40515666	12	3.3	12	86	6	57	50	4	0	45	1.23
40515720--40515750	2	15.5	2	100	0	62	51	0	0	48	1.00
40515771--40515816	23	2.0	23	86	0	65	67	13	0	19	1.23
40515994--40516056	24	2.7	22	87	7	81	38	17	7	36	1.79
40517173--40517203	2	15.5	2	100	0	62	48	0	0	51	1.00
40517474--40517553	29	2.6	30	86	5	99	32	10	13	43	1.77
40517499--40517562	30	2.2	29	82	2	74	32	10	10	45	1.74
40517705--40517762	31	1.9	30	82	3	71	36	17	10	36	1.84
40520856--40520942	25	3.5	25	79	0	93	25	28	19	26	1.99
40522921--40522955	18	1.9	18	88	0	52	37	25	0	37	1.57
40523819--40523858	11	3.5	11	83	12	53	62	0	0	37	0.95
40523810--40523870	24	2.4	25	83	8	79	60	1	0	37	1.07
40523824--40523865	13	3.1	14	83	10	61	59	0	0	40	0.97
40524372--40524413	18	2.3	18	81	18	52	38	2	2	57	1.25
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40524750--40524810	3	20.3	3	100	0	122	67	0	0	32	0.91
40526609--40526668	25	2.3	26	85	5	86	38	10	16	35	1.82
40526609--40526680	25	2.8	25	78	4	81	37	8	20	33	1.83
40532963--40533302	174	2.0	174	93	0	581	33	9	21	35	1.86
40533782--40533818	18	2.0	19	89	5	58	45	0	32	21	1.52
40537668--40537714	20	2.2	22	77	11	53	17	38	0	44	1.48
40540715--40540770	23	2.5	23	85	2	69	33	26	19	19	1.96
40545053--40545118	27	2.4	27	94	0	114	19	27	16	36	1.93
40546834--40546882	19	2.5	19	83	3	53	24	26	2	46	1.63
40548057--40548105	3	16.0	3	95	4	89	34	0	0	65	0.93

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