genome.fa.s1.2.7.7.80.10.50.1000.39.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  39  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)
12157316--12157359	15	2.9	15	86	3	61	61	0	0	38	0.96
12159608--12159857	125	2.0	125	100	0	500	36	2	24	36	1.69
12160180--12160270	39	2.3	39	88	3	130	20	14	20	43	1.87
12160218--12160334	51	2.3	51	84	1	162	19	18	20	41	1.91
12160155--12160324	90	1.9	90	87	0	250	19	19	20	40	1.92
12162858--12163052	3	65.0	3	71	6	117	31	7	1	59	1.35
12169503--12170554	44	23.6	44	77	6	775	30	19	23	27	1.98
12169503--12170554	89	11.8	88	75	8	813	30	19	23	27	1.98
12169501--12170554	222	4.7	221	83	5	1002	30	19	22	27	1.98
12169491--12170506	404	2.5	399	94	1	1741	31	19	22	26	1.98
12170693--12170741	23	2.1	23	84	0	62	38	18	30	12	1.87
12172052--12172142	6	15.3	6	76	5	60	27	7	1	63	1.28
12172053--12172142	24	3.8	24	79	1	92	27	7	1	63	1.29
12172258--12172316	12	4.8	12	83	10	66	20	6	0	72	1.06
12172986--12173347	46	8.6	44	83	12	362	29	21	13	35	1.92
12173121--12173311	36	5.0	36	84	12	247	28	20	13	37	1.91
12173029--12173347	82	3.9	82	84	12	397	29	21	13	35	1.92
12173075--12173311	118	2.0	118	94	0	420	29	20	13	36	1.92
12176259--12176486	88	2.6	88	90	0	348	29	22	24	22	1.99
12176625--12176874	44	5.5	44	68	17	145	32	18	20	28	1.96
12176605--12176786	98	1.9	97	80	6	215	32	19	19	28	1.96
12176924--12177238	50	6.3	50	70	5	197	33	23	19	23	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12176913--12177206	100	2.9	100	79	5	333	32	23	20	23	1.98
12176913--12177247	100	3.4	99	75	7	311	33	22	20	23	1.97
12185295--12185361	36	2.0	32	85	11	89	59	1	7	31	1.34
12185644--12185682	16	2.4	16	91	4	60	20	0	5	74	1.01
12189314--12189347	17	2.0	17	88	0	50	14	14	55	14	1.69
12189959--12191474	132	11.5	131	91	2	2292	27	24	19	28	1.99
12190430--12191269	44	19.1	44	61	14	149	27	24	20	28	1.99
12193781--12193819	18	2.1	18	90	4	60	66	2	15	15	1.36
12195777--12195803	13	2.1	13	100	0	54	44	25	7	22	1.79
12198968--12199096	63	2.0	63	95	0	231	35	13	13	37	1.84
12199908--12200028	61	2.0	61	85	6	163	40	3	4	52	1.37
12200213--12200284	16	4.5	16	87	0	99	27	25	5	41	1.77
12205995--12206028	11	3.1	11	91	0	50	8	11	2	76	1.12
12208735--12208768	16	2.1	16	88	0	50	8	17	23	50	1.74
12211322--12212273	253	3.8	253	95	1	1644	38	10	15	35	1.82
12222143--12222187	23	2.0	23	90	0	72	42	20	4	33	1.72
12226418--12226463	20	2.4	19	85	3	56	10	13	0	76	1.03
12226863--12226934	27	2.7	27	75	0	72	27	31	30	9	1.89
12227256--12227479	76	2.9	77	75	9	213	34	3	10	51	1.52
12227454--12227496	3	14.3	3	100	0	86	32	0	0	67	0.91
12231035--12231066	12	2.7	12	95	0	55	9	34	37	18	1.83
12234288--12235182	159	5.6	160	91	3	1353	27	9	8	53	1.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12234288--12235182	319	2.8	317	90	3	1356	27	9	8	53	1.62
12235168--12235200	17	1.9	17	93	0	57	9	9	6	75	1.18
12235185--12235234	16	3.2	16	70	13	50	22	8	4	66	1.35
12235267--12235406	67	2.0	70	86	4	196	49	11	5	33	1.63
12235483--12235571	20	4.5	20	80	8	94	0	34	0	65	0.93
12235491--12235571	10	8.1	10	78	9	67	0	33	0	66	0.92
12235784--12235840	28	2.0	30	82	6	73	35	10	7	47	1.65
12248761--12248859	28	3.6	27	84	9	119	31	12	28	28	1.92
12260996--12261059	3	21.3	3	100	0	128	65	0	0	34	0.93
12261444--12261510	24	2.8	24	74	19	68	62	1	0	35	1.04
12261402--12261510	48	2.3	47	83	10	134	59	1	2	35	1.22
12262250--12262287	6	6.5	6	87	6	60	55	0	0	44	0.99
12262349--12262417	24	3.0	23	82	16	88	36	0	1	62	1.04
12264896--12264928	16	1.9	18	88	11	52	63	12	0	24	1.28
12268061--12268121	31	2.0	30	87	3	86	42	6	13	37	1.70
12270531--12270592	22	2.7	22	90	5	88	46	1	3	48	1.28
12270566--12270607	16	2.6	16	96	0	75	47	2	4	45	1.36
12270602--12270805	111	1.8	111	93	1	356	40	8	6	44	1.60
12270825--12270890	29	2.3	29	82	7	73	24	16	16	42	1.88
12271974--12271999	13	2.0	13	100	0	52	38	15	23	23	1.92
12277279--12277309	13	2.3	14	94	5	55	74	12	0	12	1.08
12277319--12277360	16	2.8	15	89	10	68	66	11	0	21	1.23
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12277330--12277376	19	2.3	21	89	10	71	63	14	0	21	1.30
12287419--12287457	18	2.2	18	90	0	60	23	17	25	33	1.96
12295108--12295140	12	2.8	12	90	4	50	27	3	0	69	1.03
12302676--12302713	15	2.5	15	91	0	58	23	0	7	68	1.16
12302845--12302870	12	2.2	12	100	0	52	19	0	0	80	0.71
12306478--12306546	4	17.0	4	76	16	63	2	23	1	72	1.06
12306479--12306548	33	2.1	34	89	2	106	2	21	1	74	1.03
12308196--12308255	31	1.9	32	86	3	86	68	6	11	13	1.39
12308484--12308534	25	2.1	24	96	3	93	58	11	7	21	1.58
12313478--12313520	22	2.0	22	85	0	59	58	11	11	18	1.63
12327626--12327664	2	19.5	2	100	0	78	51	0	48	0	1.00
12328653--12328699	17	2.7	18	83	9	62	70	0	4	25	1.05
12328825--12328908	3	28.0	3	85	0	87	55	1	8	34	1.37
12330679--12330722	21	2.1	21	91	0	70	22	29	4	43	1.73
12330762--12331007	132	1.9	132	79	3	280	28	24	18	28	1.98
12331019--12331244	88	2.6	88	89	1	310	28	25	17	28	1.97
12330928--12331305	136	2.8	133	82	7	392	27	25	16	29	1.97
12330975--12331295	45	7.2	45	72	6	249	28	25	16	28	1.97
12331114--12331375	133	2.0	133	89	0	407	29	25	16	29	1.97
12330911--12331376	221	2.1	222	86	3	661	28	24	17	29	1.97
12343603--12343684	3	27.0	3	80	2	92	58	2	4	34	1.32
12346090--12346130	22	1.9	21	90	5	64	70	14	4	9	1.30
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12346554--12346610	17	3.2	17	78	9	51	57	1	1	38	1.19
12351408--12351446	20	2.0	20	85	10	53	46	2	2	48	1.29
12353888--12353941	20	2.8	20	78	13	58	37	0	1	61	1.07
12363487--12363534	24	2.0	24	95	0	87	37	0	39	22	1.55
12363494--12363536	12	3.6	12	81	12	61	37	0	41	20	1.53
12365764--12365814	18	2.8	18	69	0	57	15	41	3	39	1.66
12368786--12368872	33	2.7	32	76	15	88	45	18	8	27	1.77
12368847--12368904	14	4.0	15	78	12	59	36	15	8	39	1.78
12373976--12374100	45	2.8	45	86	0	160	41	18	25	14	1.88
12378743--12378788	23	1.9	25	86	8	69	26	6	2	65	1.28
12388230--12388270	18	2.3	19	84	12	52	43	0	4	51	1.23
12395771--12395812	9	4.4	9	83	16	50	76	2	0	21	0.90
12395770--12395813	10	4.5	10	82	2	54	77	2	0	20	0.88
12396413--12396454	18	2.4	17	84	15	50	35	0	7	57	1.26
12396441--12396500	20	3.0	20	82	4	68	28	6	1	63	1.29
12398309--12398342	18	2.0	18	88	11	54	32	0	14	52	1.42
12403607--12403666	22	2.8	22	85	7	70	16	23	18	41	1.90
12404293--12404384	17	5.6	17	69	19	70	55	2	2	40	1.24
12404528--12404564	18	2.1	18	89	0	56	40	2	13	43	1.58
12404972--12405010	15	2.6	15	83	0	51	35	25	33	5	1.78
12411806--12411841	13	2.7	13	91	4	54	30	0	5	63	1.17
12423119--12423173	22	2.6	21	80	11	67	18	20	21	40	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
12425762--12425909	57	2.6	57	81	6	192	23	21	10	43	1.84
12427926--12427959	17	2.0	17	88	0	50	38	8	2	50	1.49
12427970--12428009	12	3.2	12	82	3	53	42	0	0	57	0.98
12427970--12428012	11	3.7	11	84	9	50	39	0	0	60	0.97
12428198--12428229	4	7.8	4	96	3	55	21	0	3	75	0.95
12428412--12428693	112	2.6	109	89	2	404	31	17	19	31	1.95
12444036--12444075	19	2.1	19	85	0	53	55	27	2	15	1.53
12446715--12447112	91	4.4	89	86	6	546	50	10	8	31	1.67
12446729--12447099	186	2.0	186	93	1	627	49	10	9	30	1.68
12447263--12447289	7	3.9	7	100	0	54	40	0	0	59	0.98

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