genome.fa.s2.2.7.7.80.10.50.1000.62.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: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62769430

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   

This is table  62  of  206  ( 24623 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)
17535062--17535280	48	4.3	48	78	15	258	35	5	7	51	1.55
17534999--17535333	110	3.1	110	93	0	555	34	5	8	51	1.57
17535196--17535272	21	3.2	24	64	20	61	33	3	9	53	1.51
17535267--17535294	14	2.0	14	100	0	56	42	7	0	50	1.30
17537886--17537984	31	3.2	31	82	1	101	14	32	31	22	1.93
17540789--17540840	15	3.2	15	73	19	50	44	0	1	53	1.11
17548397--17548548	28	5.6	28	69	10	88	42	0	3	53	1.22
17548485--17548680	57	3.4	54	70	17	144	41	1	3	54	1.23
17548397--17548612	109	2.0	106	85	12	291	42	0	4	52	1.27
17548604--17548637	17	2.0	17	100	0	68	41	0	0	58	0.98
17548604--17548651	15	3.0	15	81	9	51	41	2	0	56	1.11
17548784--17548889	44	2.5	41	79	18	135	35	31	3	29	1.75
17548801--17548891	46	2.0	46	93	4	159	38	30	4	26	1.76
17548871--17548923	16	3.3	16	100	0	106	20	35	5	37	1.77
17549400--17549437	18	2.1	18	85	9	51	47	21	7	23	1.77
17554203--17554233	11	2.8	11	95	0	53	25	19	19	35	1.95
17557085--17557124	19	2.1	19	100	0	80	42	15	10	32	1.79
17560187--17560239	27	2.0	27	96	0	97	18	22	30	28	1.98
17560218--17560426	33	5.7	34	71	21	147	22	19	26	31	1.98
17560214--17560425	75	2.8	76	91	5	340	22	19	27	31	1.98
17561833--17561893	28	2.1	30	88	11	92	42	0	3	54	1.17
17562345--17562380	18	2.0	18	88	0	54	16	0	27	55	1.42
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
17567650--17567713	25	2.6	25	92	0	110	14	25	18	42	1.88
17567939--17568039	25	4.0	25	72	12	82	20	26	21	30	1.98
17572349--17572414	25	2.6	25	85	0	78	27	21	25	25	1.99
17575709--17575741	13	2.4	14	80	10	50	45	21	6	27	1.75
17575847--17576101	82	3.2	81	85	6	349	49	12	10	27	1.73
17575803--17576101	158	1.9	159	85	2	413	48	12	11	27	1.75
17575803--17576101	82	3.8	78	81	8	318	48	12	11	27	1.75
17577855--17577973	38	3.1	38	79	11	161	47	11	12	27	1.76
17577836--17577955	39	3.1	39	79	11	165	48	8	15	28	1.73
17583466--17583526	22	2.8	22	80	5	70	21	24	19	34	1.96
17583480--17583551	22	3.3	22	75	7	65	23	29	18	29	1.97
17587344--17587431	45	2.0	45	95	0	158	38	14	15	30	1.88
17590312--17590417	43	2.5	43	80	11	119	25	16	27	30	1.97
17599091--17599134	3	14.3	3	95	4	79	31	0	2	65	1.05
17603342--17603371	15	1.9	16	93	6	53	23	26	20	30	1.98
17609322--17609353	16	1.9	17	93	6	57	0	18	9	71	1.12
17609978--17610017	19	2.3	18	87	12	57	30	2	5	62	1.29
17610297--17610326	2	15.0	2	100	0	60	50	0	0	50	1.00
17623247--17623303	2	29.0	2	96	3	107	49	0	0	50	1.00
17625020--17625080	24	2.5	24	81	5	68	6	62	4	26	1.40
17628218--17628303	26	3.3	25	73	9	73	50	3	2	44	1.32
17633547--17633571	13	1.9	13	100	0	50	48	12	16	24	1.79
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
17636420--17636518	42	2.4	42	87	3	146	21	28	12	38	1.89
17642922--17643009	43	2.1	41	82	4	104	28	14	26	30	1.95
17642932--17643033	43	2.4	43	81	0	114	30	15	23	30	1.95
17659713--17659879	89	1.9	86	84	6	219	31	13	11	42	1.81
17659943--17660113	86	2.0	87	87	5	249	36	9	11	41	1.75
17660059--17660269	74	2.7	74	75	14	226	32	13	11	42	1.80
17659973--17660269	157	1.9	157	85	3	407	33	12	11	42	1.78
17660105--17660290	83	2.2	83	85	5	259	31	12	10	44	1.77
17666908--17666974	25	2.8	25	78	14	79	16	4	4	74	1.14
17667033--17667066	13	2.4	15	90	9	54	38	0	0	61	0.96
17667049--17667106	19	3.1	19	79	13	66	37	0	1	60	1.07
17667167--17667275	10	11.1	9	76	16	101	37	0	2	59	1.12
17667159--17667272	30	3.8	30	94	0	201	34	0	3	62	1.12
17667160--17667275	20	5.8	20	76	15	116	36	0	2	61	1.10
17667159--17667275	60	2.0	60	98	0	225	35	0	3	60	1.13
17667329--17667403	29	2.6	29	83	12	84	40	0	0	60	0.97
17672777--17672801	13	1.9	13	100	0	50	16	12	48	24	1.79
17674780--17674851	21	3.3	21	77	12	74	55	0	0	44	0.99
17674789--17674852	21	2.9	22	84	11	87	59	0	0	40	0.97
17674789--17674848	23	2.7	22	89	7	86	56	0	0	43	0.99
17674881--17674943	23	2.7	23	80	11	67	73	3	4	19	1.15
17676067--17676091	3	8.3	3	100	0	50	64	0	0	36	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
17684461--17684515	21	2.7	21	88	8	78	38	5	3	52	1.42
17695606--17695654	23	2.1	23	81	7	55	57	16	12	14	1.66
17705306--17705350	17	2.8	17	83	12	51	51	6	6	35	1.55
17707191--17707265	36	2.0	38	92	5	127	28	16	6	49	1.70
17707343--17707406	27	2.4	27	86	2	85	53	6	1	39	1.36
17707675--17707716	20	2.0	22	86	9	61	61	0	2	35	1.09
17707817--17707857	21	1.9	22	85	5	57	36	0	4	58	1.20
17707947--17708020	30	2.6	29	79	12	73	37	0	0	62	0.96
17712383--17712409	12	2.2	12	100	0	54	11	33	0	55	1.35
17728531--17728563	14	2.2	16	89	10	52	72	0	6	21	1.05
17729280--17729314	6	5.8	6	100	0	70	65	17	0	17	1.27
17732438--17732531	42	2.2	42	84	0	116	39	15	24	20	1.92
17732453--17732544	42	2.2	42	88	0	130	40	16	25	18	1.91
17732548--17732601	20	2.7	21	80	13	69	42	12	20	24	1.87
17740042--17740123	3	27.3	3	89	0	128	64	1	3	30	1.18
17741386--17741412	11	2.5	11	100	0	54	0	0	7	92	0.38
17741666--17741954	50	5.9	48	74	11	205	26	16	20	35	1.94
17741775--17741854	42	1.9	42	89	0	124	27	15	26	31	1.95
17742107--17742285	46	3.9	46	91	0	286	29	25	18	26	1.98
17743101--17743125	12	2.1	12	100	0	50	36	8	32	24	1.84
17754781--17754859	6	13.2	6	74	5	61	58	1	7	32	1.34
17754789--17754828	15	2.7	15	92	0	62	57	0	2	40	1.12
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
17754781--17754859	9	8.8	9	77	5	61	58	1	7	32	1.34
17754781--17754859	15	5.3	15	77	6	61	58	1	7	32	1.34
17755828--17755860	5	6.6	5	86	13	50	81	0	0	18	0.68
17755828--17755854	14	1.9	14	100	0	54	81	0	0	18	0.69
17755829--17755863	9	3.7	9	85	14	52	80	0	0	20	0.72
17757712--17758172	24	19.4	23	76	7	377	40	18	12	28	1.87
17757723--17758167	47	9.4	47	77	7	317	41	18	11	28	1.86
17757775--17758186	145	2.9	144	88	4	577	40	17	12	29	1.86
17758174--17758211	2	19.0	2	100	0	76	50	0	0	50	1.00
17765516--17766097	24	24.3	24	75	9	467	40	17	12	29	1.86
17765526--17766097	47	12.0	47	76	8	494	41	17	12	29	1.85
17765537--17766089	71	7.7	69	76	7	478	41	17	12	29	1.86
17766893--17766985	43	2.2	44	78	9	102	26	30	18	24	1.98
17766914--17766995	43	1.9	43	87	0	119	28	32	17	21	1.96
17770646--17770749	55	1.9	54	88	2	154	41	0	3	53	1.25
17771353--17771518	20	8.1	20	69	21	62	59	2	3	34	1.28
17771340--17771408	10	7.0	10	71	14	54	62	1	1	34	1.13
17771384--17771465	20	4.4	19	71	21	75	64	1	4	29	1.22
17781036--17781068	6	5.3	6	92	7	57	84	0	15	0	0.61
17781036--17781068	13	2.6	13	95	4	59	84	0	15	0	0.61
17786266--17786290	12	2.1	12	100	0	50	44	32	0	24	1.54
17787344--17787376	17	1.9	17	100	0	66	54	0	18	27	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
17787848--17787955	44	2.5	44	86	8	166	43	18	20	17	1.88
17790380--17790460	7	11.7	7	94	2	137	74	0	12	13	1.08
17794420--17794465	15	2.9	15	90	6	65	23	8	2	65	1.32
17796514--17796543	11	2.7	11	89	0	51	33	0	0	66	0.92
17800019--17800123	30	3.4	31	87	7	126	41	4	0	53	1.22
17800051--17800178	30	4.5	30	80	11	119	42	3	0	53	1.22
17801584--17801613	3	10.0	3	100	0	60	33	0	33	33	1.58
17802347--17802379	15	2.2	15	94	0	57	57	3	0	39	1.14
17802345--17802382	15	2.7	14	84	8	51	55	2	0	42	1.14
17802537--17802583	21	2.2	22	88	3	69	27	2	0	70	0.99

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