genome.fa.s1.2.7.7.80.10.50.1000.134.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: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  55868233

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   

This is table  134  of  187  ( 22383 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)
40510754--40510815	33	2.0	30	84	9	79	53	0	0	46	1.00
40511668--40511791	40	3.1	39	74	3	113	37	18	19	24	1.94
40511844--40512006	41	4.0	41	95	3	267	20	22	23	33	1.97
40511844--40512006	81	2.0	82	91	3	267	20	22	23	33	1.97
40512107--40512280	41	4.2	41	93	0	303	20	22	23	33	1.97
40512107--40512300	41	4.7	40	91	2	273	19	21	23	35	1.96
40512410--40512460	26	2.0	26	84	0	66	58	5	11	23	1.55
40513890--40514060	66	2.6	65	86	4	218	40	18	27	13	1.88
40514031--40514075	21	2.1	21	87	0	63	37	15	42	4	1.67
40514039--40514082	21	2.1	21	82	0	52	34	18	43	4	1.70
40514065--40514143	21	3.8	21	82	0	95	35	15	41	7	1.75
40514451--40514747	43	6.9	43	81	0	252	25	20	27	26	1.99
40514451--40514700	129	1.9	129	83	0	320	24	19	28	27	1.98
40514451--40514765	129	2.4	128	78	3	310	24	20	26	27	1.99
40514641--40514762	43	2.8	43	83	6	131	30	27	21	20	1.98
40517828--40517935	38	2.8	38	84	0	126	32	17	13	36	1.89
40523662--40523762	52	1.9	52	97	0	193	30	46	5	16	1.71
40526240--40526271	15	2.2	15	94	5	57	50	0	18	31	1.48
40530969--40531091	42	3.0	41	80	5	149	32	25	13	28	1.94
40531433--40531474	21	2.0	21	95	0	75	30	19	2	47	1.62
40532533--40532571	18	2.2	18	90	0	60	15	17	46	20	1.84
40532565--40532602	17	2.2	17	95	0	67	18	21	36	23	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40552731--40552757	2	13.5	2	100	0	54	51	0	0	48	1.00
40555396--40555440	5	8.8	5	85	4	63	77	0	22	0	0.76
40556038--40556067	5	6.0	5	100	0	60	40	40	0	20	1.52
40556390--40556436	21	2.2	21	88	0	67	38	27	2	31	1.69
40559839--40559870	16	1.9	17	93	6	57	50	6	0	43	1.27
40559838--40559879	17	2.5	16	84	7	57	52	4	2	40	1.35
40560048--40560081	17	2.0	17	88	11	52	76	5	0	17	0.98
40560275--40560326	27	1.9	27	88	0	77	40	17	0	42	1.49
40564706--40564760	16	3.4	16	76	2	65	34	7	16	41	1.76
40570648--40570687	9	4.4	9	96	0	62	40	25	10	25	1.86
40570886--40571002	39	3.0	39	89	1	191	17	4	28	49	1.66
40570983--40571007	13	1.9	13	100	0	50	12	0	48	40	1.40
40571591--40571624	16	2.2	15	89	5	50	55	2	0	41	1.15
40571691--40571746	29	1.9	29	82	7	69	51	16	7	25	1.69
40579234--40579294	27	2.2	28	75	13	65	49	1	1	47	1.21
40582416--40582495	29	2.7	30	73	5	83	33	23	17	25	1.96
40590731--40590773	2	22.0	2	95	4	79	48	0	0	51	1.00
40593689--40593782	36	2.6	36	93	0	152	19	12	44	23	1.85
40593766--40593875	33	3.3	33	87	2	141	24	9	51	14	1.71
40593820--40593874	15	3.5	15	72	13	56	29	9	50	10	1.68
40593805--40593863	18	3.5	17	71	15	59	27	5	50	16	1.66
40598276--40598319	22	2.0	22	100	0	88	27	9	22	40	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40603659--40603841	51	3.6	51	87	0	258	42	19	18	19	1.90
40603762--40603790	6	4.8	6	100	0	58	48	17	17	17	1.82
40604240--40604289	25	2.0	25	84	11	66	36	22	0	42	1.54
40605314--40605368	8	6.8	8	73	19	51	60	1	0	38	1.08
40612711--40612775	34	1.9	34	90	0	103	29	18	12	40	1.87
40612711--40612794	34	2.5	35	86	2	100	29	16	11	41	1.84
40613631--40613657	2	13.5	2	100	0	54	51	0	0	48	1.00
40613877--40613946	30	2.3	29	83	9	79	44	2	2	50	1.31
40615250--40615280	16	1.9	16	93	0	53	45	3	0	51	1.17
40615501--40615542	15	2.8	15	85	0	57	59	0	0	40	0.97
40615566--40615598	16	1.9	18	88	11	52	45	6	3	45	1.43
40620958--40620998	11	3.6	12	83	9	59	7	2	4	85	0.81
40620957--40620999	22	2.0	22	95	0	77	9	4	4	81	0.97
40620957--40620998	10	4.0	10	85	11	57	9	2	4	83	0.88
40625457--40625504	2	24.0	2	100	0	96	50	0	0	50	1.00
40627289--40627395	41	2.6	41	89	0	160	21	22	3	52	1.63
40628463--40628505	19	2.3	19	96	4	79	27	18	0	53	1.45
40629521--40629587	30	2.2	30	91	0	116	29	28	23	17	1.97
40633737--40633770	17	1.9	18	88	5	52	38	11	5	44	1.65
40636574--40636734	87	1.9	86	84	3	216	38	21	13	26	1.91
40644972--40645016	19	2.3	20	81	7	58	66	4	0	28	1.11
40651501--40651537	18	2.0	19	89	5	58	2	62	0	35	1.10
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40651499--40651540	18	2.4	17	84	11	57	2	57	0	40	1.12
40655879--40656023	43	3.4	43	75	10	136	30	13	26	29	1.94
40655888--40656045	85	1.9	85	80	7	187	30	13	25	30	1.94
40658537--40658662	66	1.9	66	93	3	218	21	25	6	46	1.74
40658795--40658850	21	2.6	21	88	5	76	23	28	1	46	1.62
40664497--40664533	10	3.5	11	89	10	60	78	0	21	0	0.75
40664497--40664534	14	2.8	14	96	4	69	78	0	21	0	0.74
40674085--40674109	13	1.9	13	100	0	50	16	32	16	36	1.90
40675941--40676107	90	1.9	90	79	5	194	35	14	21	28	1.93
40675905--40676125	90	2.5	90	70	8	191	36	13	20	29	1.91
40685927--40686408	238	2.0	239	93	0	831	33	14	21	31	1.93
40687839--40687968	56	2.3	54	75	12	127	39	2	3	54	1.31
40691870--40691910	4	10.2	4	89	0	64	2	0	21	75	0.92
40697142--40697211	32	2.2	31	85	5	95	38	15	15	30	1.89
40699899--40699947	21	2.3	21	79	6	55	30	38	22	8	1.83
40700198--40700223	13	2.0	13	100	0	52	38	46	0	15	1.46
40700391--40700444	15	3.8	15	71	14	60	46	29	0	24	1.53
40700211--40700414	43	4.7	44	91	1	333	44	30	0	24	1.58
40700211--40700414	22	9.4	22	90	2	333	44	30	0	24	1.58
40700211--40700414	65	3.1	66	91	2	333	44	30	0	24	1.58
40700456--40700490	18	1.9	18	88	0	52	48	34	0	17	1.47
40700493--40700718	53	4.2	53	77	10	249	46	7	6	39	1.56
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40700595--40700725	43	2.9	46	74	19	132	48	7	3	39	1.50
40703768--40704208	125	3.5	124	90	1	704	30	21	17	30	1.96
40706218--40706271	27	2.0	27	96	0	99	31	12	22	33	1.92
40708969--40709033	32	2.0	32	96	0	121	27	4	24	43	1.74
40711544--40711572	2	14.5	2	100	0	58	48	0	0	51	1.00
40713007--40713042	16	2.2	16	90	0	54	47	2	2	47	1.31
40717887--40718049	42	3.8	42	78	7	159	26	15	16	41	1.89
40717901--40718049	43	3.5	42	79	8	122	27	15	16	40	1.88
40718702--40718759	23	2.5	23	76	15	66	36	17	12	34	1.87
40723821--40723868	19	2.5	19	86	3	69	47	6	0	45	1.27
40730983--40731370	45	8.9	43	78	9	288	29	21	23	25	1.99
40731916--40731977	19	3.3	19	95	0	115	37	8	16	38	1.78
40731965--40731989	12	2.1	12	100	0	50	40	0	16	44	1.47
40731979--40732023	23	2.0	23	86	4	65	37	6	17	37	1.76
40732424--40732463	2	20.5	2	84	5	55	45	0	2	52	1.14
40734353--40734408	26	2.1	27	90	6	87	33	3	10	51	1.54
40734330--40734408	14	5.6	14	74	14	72	35	3	11	49	1.57
40735335--40735422	11	9.1	9	70	20	54	67	2	3	27	1.19
40735339--40735394	21	2.7	19	76	15	58	71	3	3	21	1.17
40735381--40735414	8	4.1	8	88	3	50	70	0	0	29	0.87
40735336--40735489	9	16.4	9	67	24	54	66	2	3	26	1.22
40735443--40735487	19	2.4	19	88	0	63	66	4	2	26	1.22
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
40735460--40735513	19	2.9	18	83	2	54	62	1	5	29	1.28
40744693--40744719	3	9.0	3	100	0	54	66	0	33	0	0.92
40746494--40746541	18	2.6	18	76	3	51	52	0	0	47	1.00
40746503--40746549	20	2.1	24	81	14	57	46	0	2	51	1.13
40748490--40748531	16	2.6	16	80	0	57	14	0	26	59	1.35
40748963--40749003	2	20.5	2	100	0	82	51	0	0	48	1.00
40749207--40749509	90	3.2	95	84	9	406	39	16	1	42	1.59
40757467--40757524	26	2.2	26	81	6	64	20	17	20	41	1.90
40757514--40757572	25	2.4	25	85	2	75	13	27	25	33	1.93
40758994--40759044	24	2.1	24	96	0	93	21	17	15	45	1.86

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