genome.fa.s8.2.7.7.80.10.50.1000.2.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: Chr08 ID=Chr08-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  57128820

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   

This is table  2  of  190  ( 22705 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)
317849--317873	11	2.3	11	100	0	50	40	0	0	60	0.97
320197--320291	49	1.9	49	89	4	147	43	8	22	26	1.81
320379--320485	52	2.0	53	89	5	164	40	11	19	28	1.86
322529--322572	20	2.2	20	88	4	63	6	22	6	63	1.43
323487--323630	78	1.8	78	84	0	198	34	25	15	24	1.94
327496--327599	49	2.1	49	92	0	172	31	7	11	49	1.67
328983--329025	21	2.0	21	91	8	70	34	0	9	55	1.32
329168--329256	45	2.0	44	87	10	128	38	24	4	32	1.76
329421--329484	34	1.9	33	84	9	85	51	1	1	45	1.20
329851--329904	17	3.0	18	81	8	65	53	0	1	44	1.11
330331--330442	19	5.9	19	73	4	75	28	4	3	63	1.31
330414--330450	19	1.9	19	89	10	58	32	2	0	64	1.07
331848--331931	38	2.4	34	84	11	100	46	13	8	32	1.72
334034--334234	97	2.1	97	85	0	267	26	12	31	29	1.93
335148--335244	34	2.8	33	84	6	131	46	13	10	29	1.76
335403--335427	12	2.1	12	100	0	50	48	0	24	28	1.52
337958--338143	92	2.0	91	84	3	239	34	15	19	30	1.93
340744--340773	14	2.1	14	100	0	60	50	16	6	26	1.70
340795--340837	2	21.5	2	95	0	77	48	0	0	51	1.00
342412--342443	16	2.0	17	88	11	50	31	0	0	68	0.90
342428--342493	28	2.4	28	73	16	66	37	3	3	56	1.30
352917--353291	198	1.9	198	80	7	449	37	21	11	29	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
364779--364834	21	2.7	20	83	8	58	26	30	1	41	1.66
364794--364834	20	2.0	20	85	4	55	34	29	0	36	1.58
368912--368936	13	1.9	13	100	0	50	48	0	8	44	1.32
372438--372560	59	2.1	59	83	5	153	29	10	21	38	1.87
375298--375389	29	3.2	29	77	9	116	19	1	23	55	1.50
377220--377259	15	2.7	15	84	0	53	32	22	12	32	1.91
379541--379702	46	3.6	46	93	2	267	33	14	22	29	1.94
385361--385410	24	2.1	24	82	14	59	64	4	4	28	1.30
385926--385955	6	5.0	6	95	0	51	33	46	16	3	1.64
393314--393395	3	27.3	3	100	0	164	67	0	0	32	0.91
393524--393548	7	3.6	7	100	0	50	44	0	0	56	0.99
400148--400203	29	1.9	29	92	0	94	55	7	1	35	1.38
422212--422287	23	3.3	23	96	0	143	21	21	26	31	1.98
443593--443670	39	2.0	39	89	0	120	43	10	10	35	1.73
445823--445879	3	19.0	3	100	0	114	66	0	0	33	0.92
457927--457966	20	2.0	20	90	0	62	27	10	12	50	1.72
457912--457978	34	1.9	35	90	3	109	31	8	13	46	1.74
457906--457982	14	5.0	15	71	20	52	33	9	14	42	1.77
458796--458857	30	2.0	32	87	6	92	22	6	3	67	1.28
467700--467775	29	2.6	29	82	4	89	48	14	13	23	1.79
473092--473141	22	2.3	22	80	13	59	22	24	2	52	1.58
498505--498563	28	2.2	25	82	8	64	32	10	1	55	1.43
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
513811--513866	20	2.9	18	82	12	58	57	1	0	41	1.09
513963--513999	10	3.5	11	85	7	51	67	0	2	29	1.04
514033--514137	46	2.3	45	83	4	122	33	6	4	55	1.47
514104--514174	19	3.8	18	76	9	61	29	2	4	63	1.27
514292--514502	92	2.3	92	85	4	266	36	7	18	37	1.79
514293--514502	91	2.3	92	83	4	264	36	7	19	37	1.79
527170--527224	19	2.7	20	83	11	67	70	1	3	23	1.12
527267--527308	21	2.0	22	85	4	59	57	0	7	35	1.26
527328--527361	15	2.3	15	89	0	50	67	0	2	29	1.05
536326--536356	16	1.9	16	100	0	62	54	0	0	45	0.99
540250--540299	26	2.0	25	92	7	84	44	8	0	48	1.32
540451--540628	18	10.0	17	72	16	82	67	0	32	0	0.95
540453--540524	10	6.6	10	73	17	54	68	0	31	0	0.90
540453--540629	24	7.5	23	66	20	82	68	0	31	0	0.94
540456--540630	28	6.0	28	68	22	87	68	0	30	0	0.94
540471--540630	38	4.3	37	83	10	177	68	0	30	0	0.94
540473--540573	10	10.5	10	72	16	79	65	0	33	0	1.00
540487--540629	18	7.5	19	69	20	86	67	0	31	0	0.95
541630--541666	17	2.2	17	100	0	74	29	16	8	45	1.76
542632--542660	14	2.1	14	100	0	58	37	6	0	55	1.27
545040--545077	18	2.1	18	90	0	58	15	44	5	34	1.69
545043--545084	18	2.3	18	83	0	57	21	47	2	28	1.63
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
545790--545836	3	15.7	3	100	0	94	65	0	0	34	0.93
546127--546228	27	3.8	27	81	0	87	11	41	23	23	1.87
546254--546286	13	2.7	12	95	4	57	0	3	9	87	0.63
546256--546286	12	2.6	12	94	0	53	0	3	6	90	0.55
552675--552717	16	2.6	16	77	3	50	44	6	4	44	1.52
558900--558941	21	2.0	22	81	13	52	47	0	2	50	1.14
563038--563086	13	3.5	13	78	21	55	69	0	0	30	0.89
563039--563076	17	2.4	16	86	8	51	71	0	0	28	0.87
570787--570817	16	2.0	15	93	6	53	67	0	0	32	0.91
571625--571667	20	2.2	20	95	0	77	32	2	23	41	1.67
577538--577670	66	2.0	66	100	0	266	29	13	21	36	1.91
582406--582578	85	2.0	84	82	5	206	33	16	23	26	1.95
583024--583348	168	1.9	168	83	1	418	29	24	28	18	1.98
583458--583534	11	6.8	11	70	20	52	41	3	0	54	1.19
583518--583667	58	2.6	59	74	15	141	43	4	5	46	1.47
584057--584097	2	20.5	2	100	0	82	48	0	0	51	1.00
589018--589077	30	2.0	30	90	0	93	41	13	20	25	1.88
590150--590202	22	2.6	19	75	18	52	62	7	0	30	1.23
592632--592658	14	1.9	14	100	0	54	44	0	7	48	1.31
595375--595422	20	2.3	20	78	7	51	75	0	16	8	1.04
609397--609436	20	2.0	20	90	0	62	27	10	12	50	1.72
609382--609448	34	1.9	35	84	3	91	34	8	10	46	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
617861--617909	20	2.5	19	80	9	62	30	2	6	61	1.32
617861--617914	21	2.7	20	77	8	56	29	1	9	59	1.39
618704--618812	53	2.1	53	100	0	218	54	7	17	21	1.67
626626--626679	26	2.0	28	85	7	76	7	29	7	55	1.55
632403--632436	14	2.5	14	95	4	61	50	35	0	14	1.44
639847--639887	20	2.0	20	85	4	55	36	0	14	48	1.44
644354--644384	9	3.4	9	90	0	53	25	12	22	38	1.90
649227--649265	19	2.0	19	85	5	51	20	10	28	41	1.85
652897--652947	16	3.4	15	79	10	52	80	5	5	7	1.02
661353--661399	2	23.5	2	82	0	58	48	6	2	42	1.40
663589--663688	50	2.0	47	80	14	105	54	9	7	30	1.58
665578--665622	21	2.1	21	87	0	63	40	2	31	26	1.68
665599--665693	33	2.8	34	78	12	113	42	1	26	30	1.62
671303--671356	15	3.3	15	74	18	54	44	0	1	53	1.11
671427--671482	13	4.4	13	71	10	53	50	0	0	50	1.00
671419--671480	22	2.9	22	80	2	63	51	0	1	46	1.10
671522--671566	22	2.0	22	83	8	56	44	0	2	53	1.13
674050--674087	20	1.9	20	88	0	58	36	0	0	63	0.95
674123--674169	3	15.7	3	100	0	94	34	0	0	65	0.93
674448--674478	16	1.9	16	93	0	53	41	0	3	54	1.16
679780--679820	21	1.9	22	85	5	57	7	46	4	41	1.53
696309--696345	19	1.9	19	88	0	56	67	0	0	32	0.91
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
705279--705486	62	3.1	67	75	20	218	41	3	4	50	1.40
705387--705438	24	2.4	21	82	17	63	44	1	0	53	1.11
705351--705467	32	3.7	32	71	17	102	42	2	3	51	1.32
707713--707785	31	2.4	29	80	12	85	49	6	17	26	1.72
708254--708304	2	25.5	2	100	0	102	49	0	0	50	1.00
713088--713121	3	11.3	3	100	0	68	67	0	32	0	0.91
717020--717062	2	22.0	2	95	4	79	48	0	0	51	1.00
718402--718462	31	2.0	29	84	9	77	29	0	3	67	1.07
720949--720979	2	16.0	2	93	6	55	51	0	0	48	1.00
720975--721018	21	2.1	21	91	0	70	47	6	6	38	1.57

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