genome.fa.s4.2.7.7.80.10.50.1000.9.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: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

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   

This is table  9  of  198  ( 23681 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)
3142081--3142243	60	2.7	59	81	9	188	36	17	9	37	1.81
3149707--3149760	22	2.4	22	78	9	56	59	22	1	16	1.47
3151138--3151197	15	4.1	14	75	12	57	83	0	1	15	0.73
3151132--3151199	10	6.7	10	75	14	59	80	0	1	17	0.78
3151132--3151199	18	4.0	17	79	11	77	80	0	1	17	0.78
3157492--3157992	110	4.6	110	92	1	792	34	19	14	30	1.92
3157502--3157992	221	2.2	219	92	1	813	34	19	14	30	1.92
3158146--3158213	28	2.3	29	80	12	77	69	8	4	17	1.32
3158179--3158243	22	2.9	23	77	11	64	70	6	7	15	1.30
3159704--3159733	15	1.9	16	93	6	53	30	6	33	30	1.83
3160094--3160181	40	2.2	40	83	6	106	32	14	19	32	1.92
3160228--3161535	100	13.1	100	89	0	1917	22	20	24	32	1.98
3162615--3162758	43	3.4	43	85	6	170	30	21	14	33	1.93
3163991--3164029	20	2.0	20	85	10	53	0	23	0	76	0.78
3166852--3167462	110	5.6	108	93	1	997	34	19	16	29	1.94
3166852--3167462	221	2.8	219	93	1	1019	34	19	16	29	1.94
3167607--3167665	4	15.0	4	74	10	50	69	5	3	22	1.23
3167607--3167682	23	3.3	23	75	17	77	71	5	3	19	1.22
3168570--3168594	12	2.1	12	100	0	50	16	52	24	8	1.70
3168718--3168754	20	1.9	20	94	5	67	75	0	16	8	1.02
3170059--3170114	27	2.1	27	96	0	103	33	7	19	39	1.79
3171410--3171507	23	4.3	23	93	2	171	31	25	22	20	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3171410--3171507	45	2.2	46	92	3	171	31	25	22	20	1.98
3171733--3171770	17	2.2	17	86	9	51	42	21	2	34	1.67
3178979--3179099	23	5.3	23	94	2	217	31	25	22	20	1.98
3178978--3179099	45	2.7	46	93	2	219	31	25	22	20	1.98
3179325--3179362	17	2.2	17	86	9	51	42	21	2	34	1.67
3190618--3190690	32	2.3	32	85	0	92	27	12	13	46	1.79
3192802--3192879	40	2.0	40	92	0	129	28	11	32	28	1.92
3204748--3204786	19	2.1	19	100	0	78	35	20	23	20	1.96
3208370--3208440	34	2.1	34	97	0	133	35	14	23	26	1.93
3211254--3211280	14	1.9	14	100	0	54	44	7	25	22	1.79
3211979--3212157	91	2.0	91	88	0	268	41	8	21	27	1.83
3216349--3216392	20	2.2	20	91	0	70	40	0	2	56	1.11
3217699--3217761	29	2.2	29	91	0	99	23	41	12	22	1.88
3221074--3221114	11	3.6	11	83	3	55	7	9	0	82	0.83
3224723--3224760	14	2.7	14	80	15	51	68	0	0	31	0.90
3227388--3227425	5	7.4	5	94	5	67	60	0	0	39	0.97
3227390--3227448	15	3.8	16	75	16	61	55	0	0	44	0.99
3227388--3227447	16	3.8	16	81	14	72	56	0	0	43	0.99
3227387--3227448	26	2.4	26	81	10	74	54	0	0	45	0.99
3227419--3227468	21	2.4	22	86	6	68	50	0	2	48	1.12
3228914--3228964	13	3.9	13	82	10	68	31	7	25	35	1.85
3231316--3231374	28	2.1	28	100	0	118	30	18	10	40	1.84
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3232237--3232275	19	2.1	18	85	4	51	61	5	0	33	1.18
3233112--3233154	6	7.2	6	100	0	86	81	0	0	18	0.69
3237387--3237815	212	2.0	210	95	2	781	27	17	20	34	1.95
3238746--3238789	23	2.0	23	86	4	63	29	4	2	63	1.26
3243531--3243556	8	3.2	8	100	0	52	38	23	11	26	1.89
3264333--3264468	33	4.1	32	81	11	166	52	11	5	30	1.60
3264338--3264432	31	3.0	31	89	3	145	50	11	6	31	1.63
3270349--3270433	42	2.0	42	100	0	170	48	7	16	28	1.72
3271973--3272007	15	2.3	15	100	0	70	42	5	40	11	1.65
3277186--3277239	17	3.2	17	73	26	60	40	0	1	57	1.09
3277448--3277486	18	2.2	18	86	9	53	0	15	2	82	0.79
3286352--3286585	115	2.0	115	99	0	459	41	17	13	27	1.86
3292341--3292431	30	3.0	30	85	0	128	36	7	18	37	1.80
3296438--3297066	85	7.1	85	71	14	271	27	11	14	46	1.79
3296741--3297243	261	1.9	261	81	4	595	26	11	15	46	1.80
3296812--3297130	172	1.9	172	82	5	412	28	11	15	44	1.82
3296444--3299112	90	29.9	89	72	11	1485	27	11	14	47	1.78
3296530--3299090	275	9.6	266	71	13	923	27	11	14	46	1.78
3297680--3299071	176	7.8	177	73	10	694	27	10	13	48	1.75
3297960--3298932	178	5.4	185	74	11	444	27	10	14	47	1.77
3297776--3299090	91	14.6	92	72	10	354	27	10	13	47	1.77
3298906--3299067	86	1.9	86	81	6	195	27	7	15	50	1.70
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3298970--3299266	159	1.9	157	81	6	359	24	11	15	48	1.78
3299248--3299410	90	1.8	89	82	1	209	31	11	11	46	1.74
3299249--3299666	86	4.8	87	72	13	237	28	8	13	49	1.71
3299179--3299754	89	6.6	87	73	11	344	27	9	13	50	1.71
3299359--3299754	175	2.3	168	79	12	406	26	8	13	52	1.68
3307185--3307215	15	2.1	15	100	0	62	32	19	6	41	1.77
3312144--3312274	44	3.0	44	89	1	201	31	22	22	23	1.99
3315658--3315692	15	2.4	14	90	9	61	71	0	28	0	0.86
3325548--3325581	17	2.0	17	88	11	52	76	2	14	5	1.09
3331616--3331679	32	2.0	31	84	3	83	56	7	3	32	1.44
3339195--3339796	114	5.3	113	74	8	533	33	16	20	28	1.95
3339200--3339792	227	2.6	226	89	3	870	33	16	21	29	1.95
3339578--3339968	189	2.1	189	91	0	631	30	15	22	30	1.95
3339720--3339871	74	2.0	75	84	3	200	34	15	20	29	1.94
3340399--3340435	7	5.6	7	87	12	60	16	0	51	32	1.45
3340399--3340435	12	2.9	12	92	8	56	16	0	51	32	1.45
3340404--3340456	19	2.7	20	85	5	63	20	0	45	33	1.52
3340399--3340450	26	2.0	26	84	0	68	21	0	46	32	1.52
3340534--3340644	7	15.9	7	80	7	127	18	0	49	30	1.54
3340611--3340799	95	2.0	96	82	4	229	26	1	29	41	1.65
3340871--3340911	14	2.7	15	88	7	57	51	0	7	41	1.30
3340934--3340974	18	2.3	18	91	4	66	82	0	4	12	0.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3341449--3341857	198	2.1	196	88	3	608	28	16	20	33	1.95
3343135--3343178	18	2.4	19	84	3	54	13	15	13	56	1.67
3343182--3343268	7	12.3	7	82	2	111	4	13	11	70	1.32
3343182--3343268	21	4.1	21	86	1	129	4	13	11	70	1.32
3343504--3343736	116	2.0	116	100	0	466	33	15	12	37	1.86
3343785--3344092	100	3.1	100	96	2	577	39	7	3	49	1.46
3343789--3344092	98	3.1	98	97	1	565	39	7	3	50	1.47
3343913--3344061	48	3.1	46	68	26	137	38	7	3	50	1.47
3344162--3344213	13	4.0	13	92	0	77	46	9	1	42	1.47
3344181--3344316	53	2.6	53	85	0	200	38	11	5	45	1.62
3344461--3344702	9	27.8	9	70	12	148	45	20	3	30	1.67
3344612--3344670	24	2.4	24	83	11	75	47	18	3	30	1.65
3350263--3350395	67	2.0	66	84	8	171	41	18	26	14	1.88
3350382--3350454	21	3.5	21	77	3	67	34	16	41	8	1.78
3350437--3350494	21	2.8	21	91	0	89	32	15	46	5	1.68
3350858--3351067	43	4.9	42	80	9	210	22	17	31	28	1.97
3350858--3351073	87	2.5	86	87	3	283	22	17	31	29	1.96
3351491--3351533	22	2.0	22	95	0	77	41	27	20	9	1.83
3359011--3359054	11	3.9	11	85	5	61	31	0	2	65	1.05
3365764--3365792	2	14.5	2	100	0	58	0	51	0	48	1.00
3365792--3365840	2	24.5	2	95	0	89	48	48	0	2	1.12
3367833--3367883	20	2.6	20	75	12	52	45	1	17	35	1.60
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3368969--3369045	39	2.0	38	82	12	95	15	14	3	66	1.40
3368969--3369045	37	2.0	39	82	12	97	15	14	3	66	1.40
3370817--3370859	22	2.0	22	90	9	70	32	0	0	67	0.91
3371432--3371458	8	3.4	8	100	0	54	11	11	25	51	1.70
3376435--3376487	28	1.9	26	85	11	70	26	1	3	67	1.17
3378337--3378401	31	2.1	31	91	2	105	58	13	3	24	1.50
3378894--3378966	27	2.7	27	80	4	85	39	19	23	17	1.92
3382774--3382894	42	2.9	42	86	0	179	30	26	12	30	1.93
3383811--3383850	14	2.9	14	84	0	53	32	7	17	42	1.77
3383834--3383873	20	2.0	20	90	0	62	27	10	12	50	1.72

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