genome.fa.s9.2.7.7.80.10.50.1000.180.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: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  70713020

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   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226   

This is table  180  of  226  ( 27023 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)
57645452--57645668	30	7.2	30	78	4	150	21	24	17	35	1.95
57660632--57660666	11	3.3	11	88	4	54	20	5	0	74	1.02
57665495--57665582	32	2.8	32	80	0	104	17	26	23	32	1.96
57665801--57665842	17	2.5	17	84	0	57	19	28	33	19	1.96
57666317--57666390	37	2.0	36	82	15	89	74	2	18	4	1.10
57674073--57674103	3	10.3	3	100	0	62	67	0	0	32	0.91
57674552--57674611	25	2.6	22	76	20	68	50	1	0	48	1.11
57678774--57678877	26	4.0	27	81	8	119	20	12	26	40	1.88
57683639--57683713	38	2.0	38	100	0	150	30	10	18	40	1.85
57686615--57686870	26	9.9	26	76	3	185	17	14	27	39	1.90
57686625--57686842	78	2.8	78	80	4	219	17	14	27	40	1.88
57686615--57686842	52	4.4	52	82	2	219	17	14	27	40	1.89
57693652--57693691	18	2.3	17	87	12	55	5	40	0	55	1.22
57698440--57698502	20	3.2	20	71	15	67	17	22	23	36	1.95
57708453--57708482	15	2.0	15	93	0	51	30	0	13	56	1.37
57709473--57709577	49	2.1	49	94	1	183	41	21	10	25	1.85
57719060--57719084	8	3.1	8	100	0	50	24	36	12	28	1.91
57737521--57737559	18	2.2	18	95	0	69	25	12	5	56	1.57
57738135--57738245	40	2.8	40	84	4	136	36	22	24	17	1.95
57738301--57738649	41	8.5	41	84	2	407	19	18	27	34	1.95
57741289--57741329	20	2.0	20	100	0	82	34	4	19	41	1.73
57742953--57743141	43	4.4	43	87	2	263	21	19	32	26	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57744966--57745164	41	4.8	41	77	3	159	33	22	19	24	1.97
57744978--57745164	84	2.3	82	81	3	196	32	22	19	24	1.98
57745135--57745278	45	3.3	42	81	8	148	26	26	17	29	1.97
57744971--57745278	43	7.3	42	74	7	196	29	24	19	26	1.98
57745646--57745696	21	2.4	21	90	0	75	1	45	17	35	1.60
57750969--57751003	15	2.2	16	85	15	54	48	11	0	40	1.39
57750975--57751003	15	1.9	15	100	0	58	48	13	0	37	1.43
57751624--57751661	20	1.9	20	94	0	67	57	7	0	34	1.28
57751862--57751897	15	2.3	16	90	4	56	36	2	0	61	1.11
57752033--57752085	14	3.8	13	78	9	52	45	37	1	15	1.57
57752885--57753207	114	2.8	112	82	12	390	24	20	19	35	1.95
57752937--57753207	114	2.4	114	94	0	470	25	18	18	37	1.94
57759079--57759121	12	3.6	11	81	12	50	25	4	4	65	1.32
57768688--57768721	3	11.3	3	100	0	68	67	0	0	32	0.91
57780432--57780556	42	3.0	42	82	5	144	30	23	20	26	1.98
57781388--57781416	13	2.1	14	93	6	51	55	10	0	34	1.34
57786464--57786576	9	12.6	9	72	12	54	37	0	14	48	1.44
57786456--57786540	36	2.4	36	97	0	161	36	0	15	48	1.45
57786483--57786592	54	2.1	54	94	3	197	36	0	14	49	1.44
57787423--57787462	19	2.3	17	87	12	55	12	10	5	72	1.26
57788823--57788967	41	3.5	41	94	0	245	22	28	22	27	1.99
57788821--57788997	82	2.2	83	84	7	236	24	27	20	28	1.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57790006--57790034	14	2.1	14	100	0	58	44	20	6	27	1.77
57791024--57791048	13	1.9	13	100	0	50	68	24	0	8	1.16
57796687--57796836	41	3.7	41	89	3	230	23	29	20	26	1.99
57796685--57796861	82	2.2	83	82	9	220	25	28	19	27	1.99
57798936--57798960	13	1.9	13	100	0	50	68	24	0	8	1.16
57799222--57799247	12	2.2	12	100	0	52	23	42	0	34	1.54
57800749--57800792	22	2.0	22	82	8	54	59	11	2	27	1.44
57801883--57801924	21	2.0	21	85	0	57	35	0	30	33	1.58
57809169--57809209	2	21.0	2	92	5	66	46	0	0	53	1.00
57812480--57812508	6	4.8	6	100	0	58	17	13	0	68	1.20
57812417--57812553	69	2.0	71	89	2	215	25	17	5	51	1.68
57817180--57817205	13	2.0	13	100	0	52	15	38	15	30	1.88
57819319--57819561	70	3.5	70	85	0	333	24	25	15	34	1.95
57821196--57821226	16	1.9	16	93	0	53	54	12	0	32	1.38
57828875--57828900	2	13.0	2	100	0	52	50	0	0	50	1.00
57829867--57830011	41	3.4	43	82	7	161	28	28	17	26	1.97
57833094--57833133	6	6.8	6	82	5	55	47	0	2	50	1.14
57833104--57833138	18	1.9	18	94	0	61	48	0	2	48	1.16
57833272--57833306	18	2.0	17	94	5	61	40	0	2	57	1.14
57833606--57833669	28	2.3	27	86	7	92	56	7	1	34	1.38
57833628--57833669	14	3.1	13	83	10	57	50	7	2	40	1.43
57833599--57833671	29	2.5	30	84	6	96	53	8	1	36	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57849062--57849091	2	15.0	2	100	0	60	50	0	0	50	1.00
57849375--57849551	41	4.3	41	92	0	282	22	27	20	29	1.98
57850454--57850485	2	16.0	2	100	0	64	50	0	0	50	1.00
57852261--57852297	16	2.3	17	81	13	51	59	2	0	37	1.12
57852974--57853050	31	2.4	31	93	4	127	50	16	5	27	1.66
57858146--57858303	11	15.2	11	70	24	78	36	0	0	62	1.00
57858207--57858271	9	6.8	9	74	19	60	32	0	0	67	0.91
57858136--57858303	40	4.2	39	90	6	246	36	0	0	62	1.00
57858179--57858308	9	13.1	9	72	16	53	40	0	0	60	0.97
57858801--57858846	9	5.0	9	80	15	58	34	0	0	65	0.93
57858790--57858849	18	3.3	18	81	6	68	40	0	0	60	0.97
57861997--57862101	53	1.9	55	92	3	178	39	10	7	42	1.68
57871367--57871400	17	1.9	18	88	5	52	64	0	20	14	1.28
57871344--57871474	52	2.5	52	85	2	174	55	7	12	23	1.63
57887916--57887945	11	2.6	11	94	5	51	36	3	0	60	1.14
57890384--57890437	27	2.0	27	85	7	74	51	3	0	44	1.19
57890370--57890435	21	3.0	21	80	8	62	53	3	0	43	1.16
57890396--57890437	14	3.0	14	80	19	52	47	2	0	50	1.14
57890446--57890483	13	2.9	14	80	11	53	39	2	0	57	1.12
57896721--57896769	23	2.0	24	88	7	73	51	8	16	24	1.71
57896949--57896973	2	12.5	2	100	0	50	0	48	0	52	1.00
57901387--57901472	30	3.0	29	85	12	117	43	6	24	25	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57901385--57901473	25	3.1	30	85	12	125	41	6	25	25	1.80
57902127--57902161	17	2.0	18	88	5	54	17	11	0	71	1.14
57902479--57902588	16	6.7	16	68	19	57	34	3	1	60	1.25
57923462--57923493	16	2.0	16	100	0	64	25	12	0	62	1.30
57931905--57931958	23	2.3	23	87	0	81	38	7	27	25	1.83
57940832--57941185	41	8.7	41	81	0	323	22	27	13	36	1.92
57940995--57941059	21	3.1	21	65	12	62	20	29	16	33	1.95
57940833--57941170	123	2.7	123	82	0	372	23	26	13	35	1.92
57946251--57946327	32	2.4	32	95	2	138	46	2	22	28	1.65
57950831--57950881	20	2.5	20	87	6	68	41	13	13	31	1.84
57955397--57955434	17	2.2	17	86	13	51	26	13	0	60	1.33
57956818--57956868	20	2.5	20	87	6	68	41	13	13	31	1.84
57959135--57959202	25	2.7	26	84	4	77	25	25	20	29	1.99
57960106--57960246	43	3.3	43	89	0	201	18	31	29	19	1.96
57962668--57962710	10	4.4	10	79	5	52	67	2	2	27	1.15
57962880--57962982	9	10.6	10	70	22	60	33	2	2	60	1.27
57962878--57962982	29	3.7	29	76	10	99	34	2	2	60	1.26
57962883--57962983	19	5.3	17	71	20	60	33	2	2	60	1.27
57970961--57971022	30	2.1	30	100	0	124	43	9	6	40	1.63
57971324--57971359	12	3.0	12	87	0	54	25	0	0	75	0.81
57971359--57971395	16	2.2	18	85	9	51	70	8	0	21	1.13
57971541--57971586	11	4.3	11	80	5	58	76	13	4	6	1.14
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
57971541--57971597	21	2.7	21	83	2	60	73	12	7	7	1.23
57975143--57975220	27	2.9	27	77	11	88	30	15	30	23	1.95
57978298--57978467	41	4.1	41	96	0	295	30	21	27	20	1.98
57978270--57978467	82	2.4	82	89	0	297	30	20	25	22	1.98
57986367--57986538	44	3.8	45	79	6	181	45	15	20	19	1.85
57987783--57987845	10	5.9	10	72	20	56	74	7	15	1	1.12
57989089--57989208	55	2.2	56	82	10	140	28	23	23	25	2.00
57990509--57990537	9	3.0	10	90	10	51	20	20	0	58	1.39
58006356--58006413	26	2.3	25	81	3	71	37	22	20	18	1.94
58006378--58006427	25	2.0	25	84	7	66	32	24	24	20	1.98

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   
          209   210   211   212   213   214   215   216   217   218   219   220   221   222   223   224   
          225   226