genome.fa.s6.2.7.7.80.10.50.1000.2.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: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  51074515

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   

This is table  2  of  168  ( 20060 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)
325811--325890	39	2.1	39	97	0	151	11	5	38	45	1.62
326541--327106	216	2.6	216	89	3	861	27	23	18	29	1.98
327097--327400	129	2.4	128	90	1	466	25	23	19	31	1.98
328711--328744	17	2.0	17	88	11	52	17	17	0	64	1.29
328727--328761	7	5.1	7	86	6	54	14	17	0	68	1.21
328731--328760	13	2.3	13	94	0	51	13	16	0	70	1.18
338058--338320	69	3.8	69	81	0	274	20	20	21	37	1.94
341626--341685	22	2.6	23	76	12	61	40	5	0	55	1.22
351587--351644	22	2.7	22	79	12	66	75	3	3	17	1.07
357307--357413	41	2.6	41	91	2	180	28	20	26	24	1.99
357419--357556	42	3.3	42	79	7	127	23	15	24	36	1.94
357454--357568	43	2.7	42	78	9	126	23	17	25	33	1.96
359734--359851	61	2.0	58	88	5	173	42	3	4	50	1.38
359738--359870	58	2.2	60	83	9	157	42	3	6	48	1.43
362416--362488	25	2.9	25	87	0	92	28	19	19	32	1.96
362442--362495	25	2.2	25	86	0	72	37	20	16	25	1.93
370197--370962	279	2.7	280	84	4	963	34	13	15	35	1.87
374230--374297	34	2.0	34	85	5	93	20	26	23	29	1.99
376135--376172	20	1.9	20	88	0	58	52	0	10	36	1.36
377038--377131	37	2.4	38	87	5	127	37	9	26	26	1.87
378055--378338	70	4.0	70	83	4	334	29	12	16	41	1.84
378055--378338	74	3.9	72	81	8	308	29	12	16	41	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
378055--378338	145	2.0	144	84	0	370	29	12	16	41	1.84
378034--378339	23	12.9	23	71	9	157	30	12	16	41	1.85
378028--378339	47	6.6	47	71	7	209	30	12	16	41	1.84
381509--381537	5	5.8	5	100	0	58	17	0	0	82	0.66
381694--381776	35	2.4	35	85	4	114	7	31	10	50	1.64
382406--382792	27	14.3	27	82	4	431	42	19	20	16	1.89
382967--383037	26	2.7	26	91	0	106	16	23	19	39	1.92
385599--385659	26	2.3	26	94	0	104	37	14	13	34	1.85
385781--385838	26	2.2	26	100	0	116	31	22	15	31	1.95
394414--394464	13	4.0	13	82	5	68	15	1	1	80	0.89
394414--394470	19	3.1	18	78	14	62	17	3	1	77	1.00
394415--394462	25	1.9	25	91	0	78	14	2	2	81	0.88
394407--394471	19	3.3	20	72	12	55	23	3	1	72	1.07
395132--395211	30	2.8	30	83	12	105	35	37	0	27	1.57
395166--395213	22	2.2	21	92	3	78	35	39	0	25	1.56
395330--395361	15	2.1	16	94	5	57	46	31	0	21	1.52
395369--395402	7	4.9	7	88	0	50	26	52	2	17	1.58
396142--396300	41	3.9	41	92	0	264	28	27	23	20	1.99
396337--396471	40	3.4	40	72	8	107	19	20	21	39	1.93
399479--399505	14	1.9	14	100	0	54	44	7	11	37	1.68
399784--399960	34	5.2	34	81	4	212	18	25	14	42	1.87
399784--399960	69	2.6	67	83	5	219	18	25	14	42	1.87
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
402064--402102	12	3.1	13	88	3	53	41	0	7	51	1.31
403138--403387	87	2.9	86	85	3	304	36	12	26	24	1.91
403137--403400	29	9.1	29	78	4	212	35	14	25	24	1.93
407094--407205	57	1.9	57	87	8	165	47	6	18	27	1.73
409027--409062	3	12.0	3	100	0	72	33	0	0	66	0.92
416084--416158	38	2.0	36	87	5	105	28	14	9	48	1.75
416455--416494	3	13.3	3	100	0	80	67	0	0	32	0.91
416978--417012	18	2.1	16	89	10	52	71	11	17	0	1.14
418598--418626	3	9.7	3	100	0	58	34	0	31	34	1.58
418816--418867	24	2.2	24	85	0	68	38	3	7	50	1.50
423193--423244	24	2.2	24	85	0	68	38	3	9	48	1.54
424615--424639	13	1.9	13	100	0	50	48	0	12	40	1.40
425179--425220	16	2.7	16	77	3	50	42	2	2	52	1.27
428379--428467	45	2.0	45	93	0	151	33	24	16	24	1.96
428474--428664	51	3.8	50	81	4	231	31	29	15	23	1.95
428476--428660	101	1.8	101	89	3	291	31	29	16	23	1.96
435663--435714	26	2.0	26	100	0	104	23	15	15	46	1.83
440721--440761	16	2.5	17	84	8	57	48	0	2	48	1.14
441476--441542	9	7.4	9	84	0	80	46	20	7	25	1.77
444931--444961	2	15.5	2	100	0	62	48	0	0	51	1.00
446284--446332	17	3.0	17	82	11	59	59	0	0	40	0.98
446284--446337	22	2.5	22	80	16	69	59	1	0	38	1.08
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
453473--453524	13	4.0	13	82	7	52	59	3	0	36	1.16
456782--456912	24	5.5	24	71	17	103	38	14	12	34	1.85
456772--456918	47	3.1	47	97	0	276	39	14	11	34	1.82
457172--457206	15	2.3	15	90	9	54	51	22	0	25	1.48
464211--464240	16	1.9	16	93	6	53	36	0	13	50	1.42
467605--467650	22	2.1	22	100	0	92	30	19	13	36	1.90
479618--479693	37	2.1	36	85	11	102	38	3	3	53	1.38
479705--479820	62	1.9	60	82	5	144	41	5	4	49	1.45
481920--481964	19	2.4	18	89	10	72	48	8	17	24	1.75
497550--497574	6	4.2	6	100	0	50	32	0	0	68	0.90
498036--498095	26	2.3	26	88	2	86	28	21	23	26	1.99
502653--502741	37	2.4	37	77	3	90	33	17	15	32	1.92
505322--505400	28	2.8	28	88	0	131	26	18	26	27	1.98
505757--506030	27	10.1	27	84	2	336	17	20	20	41	1.90
507349--507387	10	3.8	10	89	3	51	41	46	0	12	1.42
512076--512111	18	2.1	17	89	5	54	16	25	11	47	1.79
512921--513025	28	3.8	28	85	0	129	32	23	23	20	1.98
513336--513663	27	12.3	27	84	3	396	17	19	19	43	1.89
521777--522061	141	2.0	141	97	0	543	40	7	4	47	1.53
521830--522048	70	3.1	70	63	16	180	40	8	3	47	1.51
528628--528660	2	16.5	2	93	0	57	48	3	0	48	1.17
529498--529598	43	2.4	42	85	5	132	22	30	10	35	1.89
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
543418--543451	16	2.1	17	88	5	52	32	14	0	52	1.42
543435--543491	20	2.8	20	83	0	78	33	10	1	54	1.45
557291--557339	22	2.1	23	81	7	55	48	2	16	32	1.57
569593--569814	41	5.4	41	91	1	340	22	28	19	29	1.98
569588--569859	122	2.2	123	86	5	365	23	27	18	30	1.98
572920--572981	25	2.5	25	91	0	97	27	24	24	24	2.00
572904--572993	25	3.7	24	80	7	92	27	23	25	23	2.00
574320--574346	11	2.5	11	100	0	54	66	7	0	25	1.17
584273--584408	50	2.7	51	87	4	195	25	16	27	29	1.97
584331--584412	26	3.2	26	65	22	73	28	14	25	31	1.95
588742--588937	56	3.5	56	77	6	193	30	20	21	28	1.98
592643--592704	23	2.8	22	85	4	63	33	20	24	20	1.97
592653--592706	23	2.4	23	90	6	85	31	18	24	25	1.97
593299--593326	3	9.3	3	100	0	56	67	0	0	32	0.91
594009--594065	5	11.4	5	80	0	69	57	0	1	40	1.09
594019--594065	15	3.1	15	90	0	76	61	0	2	36	1.08
603223--603361	38	3.7	38	83	1	181	14	17	28	39	1.89
606432--606510	29	2.7	29	82	2	95	29	13	18	37	1.90
608403--608444	15	2.7	16	82	14	52	45	0	2	52	1.13
608394--608435	15	2.9	15	82	10	52	47	0	0	52	1.00
608590--608678	45	2.0	45	89	6	137	33	28	5	32	1.80
608658--608706	16	3.1	16	90	0	80	20	32	8	38	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
609444--609503	23	2.4	26	83	10	81	33	5	0	61	1.17
615630--615725	36	2.7	36	90	1	131	42	19	7	30	1.78
615874--615988	43	2.7	42	79	15	114	28	26	19	25	1.98
625873--625899	13	2.1	13	100	0	54	22	0	22	55	1.44
627481--627684	48	4.2	48	78	5	205	23	27	20	28	1.99
627500--627677	96	1.9	96	83	2	232	23	28	20	28	1.99
629351--629547	48	4.1	48	76	2	207	27	21	28	22	1.99
629370--629545	96	1.8	96	83	0	235	26	21	30	21	1.99
633192--633252	22	2.8	22	92	0	95	34	14	26	24	1.94
641748--641894	66	2.2	66	87	2	206	42	28	10	18	1.84

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