genome.fa.s5.2.7.7.80.10.50.1000.127.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  127  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)
38955218--38955265	19	2.5	19	83	9	62	39	4	0	56	1.19
38955591--38955670	29	2.7	29	72	12	83	32	7	1	58	1.34
38956925--38956960	19	2.0	17	89	10	54	44	16	5	33	1.71
38963083--38963144	25	2.5	26	82	7	76	24	30	14	30	1.95
38967877--38967911	17	2.0	18	88	5	54	42	2	0	54	1.15
38971267--38971382	54	2.1	54	81	6	128	22	26	25	25	2.00
38971299--38971401	54	1.9	54	84	4	136	22	26	26	25	2.00
38972150--38972278	40	3.2	40	83	2	161	32	17	30	20	1.95
38972211--38972276	20	3.3	20	68	8	62	34	16	31	16	1.92
38972207--38972290	40	2.1	40	88	0	123	35	17	26	20	1.95
38972483--38972527	21	2.1	22	84	12	58	55	15	8	20	1.66
38980433--38980505	26	2.9	24	82	11	83	16	26	21	35	1.94
38990485--38990522	20	1.9	20	84	10	51	42	7	10	39	1.69
38991422--38991482	22	2.8	22	89	0	68	40	16	24	18	1.90
38991431--38991483	22	2.4	22	96	0	97	41	15	28	15	1.87
39001096--39001221	29	4.4	29	69	9	71	51	28	3	15	1.62
39008692--39008737	22	2.1	22	84	8	58	58	0	2	39	1.10
39013535--39013590	27	2.1	27	100	0	112	37	17	17	26	1.93
39021603--39021639	18	2.2	17	90	9	58	48	0	0	51	1.00
39021601--39021647	22	2.0	24	84	8	62	48	0	4	46	1.21
39021897--39022560	114	5.9	114	88	1	942	26	20	26	26	1.99
39021897--39022560	226	2.9	227	88	2	962	26	20	26	26	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39022462--39022609	71	2.1	72	87	1	208	28	17	26	27	1.98
39022766--39022828	14	4.4	14	93	2	99	25	0	39	34	1.56
39022766--39022837	28	2.6	29	84	8	105	23	0	40	36	1.55
39022766--39022837	7	10.3	7	77	4	74	23	0	40	36	1.55
39023121--39023191	15	4.9	14	77	17	65	23	1	40	33	1.64
39023503--39023574	35	2.1	35	100	0	144	44	0	20	34	1.52
39025923--39025952	15	2.0	15	93	0	51	46	0	10	43	1.37
39028181--39028213	12	2.8	12	86	4	50	27	0	9	63	1.24
39028453--39028580	43	3.0	43	82	4	152	23	22	25	28	1.99
39028653--39028694	22	1.9	22	85	0	57	45	28	16	9	1.79
39032789--39032816	1	28.0	1	100	0	56	0	0	0	100	0.00
39034433--39034507	32	2.7	25	71	24	69	53	1	1	44	1.17
39034502--39034530	14	2.1	14	100	0	58	58	0	0	41	0.98
39035210--39035235	12	2.2	12	100	0	52	7	38	23	30	1.83
39038165--39038217	18	3.0	17	86	5	70	37	1	3	56	1.28
39038377--39038469	44	2.1	46	93	4	163	36	31	4	27	1.76
39038451--39038503	16	3.3	16	91	0	88	24	33	3	37	1.74
39038562--39038620	16	3.7	15	80	6	64	32	20	1	45	1.61
39038413--39038629	116	1.9	116	82	1	274	32	25	6	35	1.82
39038766--39038808	21	2.0	20	83	16	52	67	4	2	25	1.22
39038839--39038908	34	2.0	35	83	8	90	67	4	0	28	1.10
39038837--39039010	19	9.2	19	68	18	78	62	4	0	32	1.20
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39038981--39039067	45	1.9	45	83	4	113	57	3	1	37	1.23
39039026--39039208	10	18.7	9	66	21	50	56	4	1	37	1.28
39039036--39039126	31	2.9	31	78	15	89	54	7	0	37	1.29
39039036--39039193	10	15.5	10	67	16	65	55	5	1	37	1.32
39043731--39043766	18	2.0	18	88	0	54	19	8	36	36	1.82
39047278--39047373	9	10.9	9	67	20	60	34	2	1	62	1.14
39047274--39047310	15	2.4	16	82	17	51	35	0	0	64	0.94
39050703--39050728	13	2.0	13	100	0	52	30	7	15	46	1.74
39052662--39052701	19	2.1	19	86	9	55	12	10	7	70	1.35
39053652--39053692	7	6.0	7	86	13	59	70	0	14	14	1.16
39053653--39053692	13	3.0	13	92	3	62	70	0	15	15	1.18
39054937--39055501	50	11.3	50	67	1	270	31	19	23	26	1.98
39054913--39055475	100	5.6	100	90	0	849	30	20	23	26	1.98
39055483--39055985	132	3.8	132	89	1	787	28	16	24	30	1.97
39055484--39055980	263	1.9	263	93	0	852	27	16	24	30	1.97
39070268--39070346	40	2.0	40	94	0	140	29	13	21	35	1.92
39079766--39079834	20	3.5	20	75	9	61	34	20	10	34	1.86
39081982--39082032	18	2.9	17	88	11	77	43	11	5	39	1.66
39091056--39091104	24	2.0	24	100	0	98	28	26	4	40	1.74
39099960--39100043	25	3.4	25	74	0	69	34	17	26	21	1.96
39100015--39100090	25	3.1	25	69	14	68	34	18	25	22	1.96
39100083--39100142	26	2.3	27	82	5	79	41	21	18	18	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39103642--39103673	6	5.3	6	100	0	64	81	0	0	18	0.70
39106975--39107271	139	2.1	140	88	0	443	30	22	21	24	1.99
39107490--39107687	43	4.6	43	87	2	299	29	32	17	20	1.95
39107702--39107732	16	1.9	16	93	0	53	54	0	0	45	0.99
39112418--39112471	14	3.8	14	90	2	81	35	50	0	14	1.44
39112421--39112469	21	2.3	21	85	3	62	32	53	0	14	1.41
39112421--39112469	7	6.9	7	79	11	55	32	53	0	14	1.41
39112609--39112641	14	2.3	15	94	5	59	36	33	0	30	1.58
39113042--39113316	41	6.7	41	86	2	365	28	24	21	25	1.99
39113384--39113488	39	2.7	38	85	5	138	23	20	20	35	1.96
39119771--39119868	45	2.2	45	98	0	187	19	28	11	40	1.86
39140616--39140665	20	2.6	20	87	6	68	48	14	0	38	1.44
39147572--39147610	21	1.9	20	84	5	51	61	5	17	15	1.51
39148239--39148279	21	2.0	21	85	9	57	31	26	2	39	1.70
39149976--39150019	18	2.4	18	80	0	52	20	22	9	47	1.78
39151526--39151734	97	2.1	97	82	5	251	28	16	15	38	1.90
39151416--39151853	222	2.0	223	85	2	603	27	18	15	38	1.91
39151623--39152028	125	3.2	125	88	2	589	30	17	14	37	1.89
39151623--39152028	126	3.2	124	87	4	562	30	17	14	37	1.89
39151623--39152107	252	1.9	251	78	4	528	30	17	14	38	1.89
39152391--39152793	125	3.2	125	86	2	529	29	17	15	37	1.90
39152388--39152793	127	3.2	121	85	6	506	29	16	15	38	1.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39152940--39153002	29	2.1	30	85	2	83	38	20	0	41	1.53
39153155--39153556	127	3.2	126	87	1	547	30	16	14	38	1.89
39153155--39153596	126	3.5	123	84	4	508	29	16	14	39	1.88
39151574--39153855	765	3.0	765	97	0	4246	33	17	10	37	1.85
39153683--39153750	30	2.3	29	87	7	102	39	13	0	47	1.43
39157765--39157923	54	2.9	54	84	1	212	32	19	15	32	1.93
39159005--39159051	19	2.6	17	78	21	51	57	4	29	8	1.48
39159036--39159126	33	2.8	33	86	6	114	59	5	25	9	1.51
39164496--39164749	46	5.6	46	92	1	406	35	14	20	29	1.93
39167902--39168014	37	3.1	37	78	13	117	39	2	2	54	1.28
39168044--39168076	12	2.7	13	86	13	52	48	0	0	51	1.00
39175957--39175987	15	2.1	15	93	0	53	61	6	0	32	1.21
39176539--39176589	20	2.5	22	76	20	58	37	0	1	60	1.08
39176547--39176597	10	5.0	10	75	20	52	37	0	1	60	1.08
39177502--39177807	46	6.6	47	91	1	483	38	14	19	28	1.90
39177525--39177807	93	3.0	93	96	1	523	38	14	19	27	1.91
39177502--39177807	139	2.2	140	91	1	497	38	14	19	28	1.90
39178650--39178778	43	3.0	42	81	17	174	29	29	19	21	1.98
39181100--39181167	17	4.2	16	71	17	52	54	1	2	41	1.24
39181117--39181181	33	2.0	33	81	6	78	52	1	4	41	1.31
39181401--39181467	31	2.1	32	86	13	95	16	4	1	77	1.00
39185980--39186018	19	2.1	19	85	9	53	38	2	10	48	1.51
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39188566--39188672	54	2.0	54	90	0	169	32	19	24	23	1.97
39191833--39191859	3	9.0	3	100	0	54	33	33	0	33	1.58
39195569--39195656	31	2.8	31	91	0	140	22	34	0	43	1.54
39195812--39195886	28	2.6	28	93	4	123	53	2	17	26	1.57
39197797--39197860	20	3.0	21	78	19	69	48	3	0	48	1.17
39197797--39197859	22	2.9	21	76	19	58	49	3	0	47	1.17
39199810--39199841	3	10.7	3	93	0	55	0	0	71	28	0.86
39203211--39203283	3	24.3	3	100	0	146	67	0	0	32	0.91
39203876--39203933	2	30.5	2	79	10	68	50	0	5	44	1.24
39210606--39210721	25	4.7	25	72	12	87	20	29	17	32	1.95

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   191   192   
          193   194   195   196   197   198   199   200   201   202   203   204   205   206   207   208