genome.fa.s17.2.7.7.80.10.50.1000.2.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: D04
Parameters: 2 7 7 80 10 50 1000
Length:  56598092

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   

This is table  2  of  185  ( 22116 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)
497242--497336	9	11.2	9	76	13	94	32	1	18	47	1.56
497246--497336	25	3.6	25	87	0	137	32	1	19	46	1.58
497242--497332	16	5.4	17	75	16	82	32	1	18	47	1.56
497385--497447	12	5.2	12	76	1	63	28	1	17	52	1.54
497385--497447	24	2.6	24	84	2	81	28	1	17	52	1.54
497616--497690	29	2.6	29	95	0	132	29	2	21	46	1.65
497582--497693	16	7.2	16	63	15	65	30	3	22	43	1.70
498456--498493	19	2.0	19	100	0	76	52	0	0	47	1.00
498474--498520	25	2.0	25	83	8	62	57	0	0	42	0.98
499117--499244	29	4.6	29	71	7	111	47	22	8	21	1.77
499926--500023	47	2.0	49	88	7	148	41	1	8	48	1.39
501005--501051	24	2.0	23	87	4	67	29	48	2	19	1.60
501298--501346	21	2.3	21	82	13	64	32	38	4	24	1.74
501477--501510	15	2.2	16	94	5	61	47	32	0	20	1.51
501797--501909	41	2.8	41	89	2	165	30	24	21	23	1.99
501951--502084	40	3.4	40	79	6	132	20	18	22	38	1.94
502471--502549	32	2.5	32	82	0	104	22	32	22	21	1.98
504735--504798	9	7.0	9	77	8	58	56	1	3	39	1.25
504820--504870	20	2.6	20	76	11	61	62	7	1	27	1.33
505097--505145	16	3.1	16	75	0	53	18	24	18	38	1.93
505378--505456	17	4.5	17	69	18	54	40	5	2	51	1.37
517665--517926	71	3.5	76	82	7	329	30	15	20	33	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
518081--518222	72	2.0	73	91	1	232	21	15	23	38	1.92
518073--518528	159	2.9	151	81	10	492	27	15	21	34	1.94
518232--518488	77	3.5	74	84	8	319	31	14	21	32	1.93
518646--518783	71	1.9	71	92	0	231	34	16	17	31	1.92
518555--518907	155	2.2	157	83	8	434	30	16	18	34	1.92
518788--519029	78	3.2	75	84	7	300	26	16	19	37	1.93
519009--519058	14	3.6	14	81	7	57	20	12	2	66	1.34
518855--519271	177	2.3	181	92	2	680	25	16	17	40	1.90
519186--519236	14	3.6	14	77	12	50	21	11	1	64	1.36
519200--519233	16	2.1	16	94	0	59	20	8	0	70	1.13
519308--519559	77	3.3	76	89	3	373	25	19	21	34	1.96
520271--520445	30	5.8	30	89	1	228	26	48	4	21	1.68
521089--521137	25	2.0	25	95	0	89	36	8	4	51	1.51
521259--521299	21	2.0	21	85	9	57	34	4	0	60	1.18
521288--521335	16	3.1	15	90	6	69	31	2	2	64	1.16
521288--521339	8	6.5	8	82	8	61	30	1	1	65	1.14
522577--522604	2	14.0	2	100	0	56	50	0	50	0	1.00
530380--530440	27	2.3	27	76	21	65	57	1	14	26	1.47
530933--530969	12	3.0	12	84	7	56	40	2	10	45	1.53
532806--533061	86	3.0	85	81	2	307	30	19	18	32	1.95
540530--540576	23	2.0	23	92	8	78	65	6	0	27	1.16
540546--540709	19	8.4	19	71	13	68	60	6	1	32	1.29
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
540534--540724	10	19.0	10	68	20	55	59	5	1	34	1.28
541292--541322	15	2.1	15	100	0	62	25	25	29	19	1.99
543206--543246	12	3.6	12	87	12	68	41	0	7	51	1.30
545936--545979	11	4.0	11	81	0	52	59	4	11	25	1.51
557663--557708	17	2.8	17	83	3	58	36	4	6	52	1.47
567690--567729	20	2.0	20	90	0	62	35	10	10	45	1.71
567720--567805	33	2.7	32	75	13	95	27	8	17	46	1.76
567827--567865	20	2.0	20	94	0	69	48	2	0	48	1.15
570189--570219	16	1.9	16	100	0	62	51	12	6	29	1.65
573197--573225	12	2.3	13	94	5	51	51	10	0	37	1.36
576607--576632	3	8.7	3	100	0	52	65	0	0	34	0.93
579769--579826	20	2.8	20	80	17	57	53	3	1	41	1.28
579794--579871	29	2.6	30	91	6	131	57	1	2	38	1.20
579818--579852	18	2.0	18	94	5	63	57	0	2	40	1.14
579808--579863	11	5.4	11	72	25	50	57	1	3	37	1.27
579953--580010	11	5.9	10	78	15	59	51	0	1	46	1.11
579957--580016	17	3.2	17	77	20	66	58	0	1	40	1.08
579971--580009	11	3.5	11	100	0	78	56	0	0	43	0.99
579929--579998	28	2.3	29	83	9	88	54	0	2	42	1.15
579754--579998	135	1.8	136	93	2	431	46	11	7	33	1.69
579933--580059	39	3.3	38	80	4	130	62	0	2	35	1.08
579984--580054	28	2.5	28	80	11	83	67	0	1	30	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
584245--584314	28	2.5	28	88	0	104	27	25	21	25	1.99
584341--584401	25	2.4	26	83	2	70	26	22	24	26	2.00
590698--590752	21	2.6	21	80	11	76	40	29	7	23	1.81
592589--592638	18	2.6	19	84	12	59	54	4	2	40	1.31
598374--598510	21	6.5	21	69	0	85	43	17	22	16	1.88
598369--598528	42	3.8	42	82	0	158	41	16	24	17	1.89
605069--605133	5	13.2	5	80	19	75	40	0	0	60	0.97
605069--605122	8	6.5	8	80	19	58	38	0	0	61	0.96
605072--605125	3	20.0	3	77	21	57	38	0	0	61	0.96
605069--605133	29	2.2	29	89	8	96	40	0	0	60	0.97
605142--605237	40	2.3	40	89	3	147	63	8	28	0	1.23
605445--605476	13	2.5	13	94	0	55	31	0	12	56	1.37
605571--605812	50	4.7	50	86	4	297	26	24	29	19	1.99
605571--605820	100	2.4	103	88	6	364	26	24	29	20	1.99
607806--607830	12	2.1	12	100	0	50	48	0	12	40	1.40
608258--608285	13	2.2	13	100	0	56	21	7	25	46	1.76
610223--610287	5	13.2	5	80	19	75	40	0	0	60	0.97
610223--610276	8	6.5	8	80	19	58	38	0	0	61	0.96
610226--610279	3	20.0	3	77	21	57	38	0	0	61	0.96
610223--610287	29	2.2	29	89	8	96	40	0	0	60	0.97
610296--610391	40	2.3	40	89	3	147	63	8	28	0	1.23
610599--610630	13	2.5	13	94	0	55	31	0	12	56	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
610725--610966	50	4.7	50	86	4	297	26	24	29	19	1.99
610725--610974	100	2.4	103	88	6	364	26	24	29	20	1.99
612362--612440	25	3.2	23	63	16	59	25	12	18	43	1.86
622965--622998	16	2.1	16	88	0	50	50	14	17	17	1.79
625799--625839	21	2.0	21	90	0	64	29	21	29	19	1.98
627745--627778	16	2.1	16	88	0	50	50	14	17	17	1.79
654090--654115	11	2.4	11	100	0	52	38	7	0	53	1.30
654101--654173	31	2.3	32	86	4	96	32	1	1	64	1.11
654101--654180	32	2.5	31	83	2	97	32	1	1	65	1.09
661851--661918	9	7.7	9	77	12	52	35	2	4	57	1.34
663167--663257	39	2.3	40	83	7	105	35	6	19	38	1.78
663440--663588	45	3.3	45	77	0	156	21	15	17	45	1.85
664957--665002	20	2.2	20	84	3	56	30	2	2	65	1.16
664971--665022	20	2.7	20	82	11	63	28	3	0	67	1.08
664971--665021	19	2.7	20	81	9	61	29	3	0	66	1.09
664971--665027	19	2.9	19	78	17	55	28	7	0	64	1.19
665080--665152	30	2.6	28	79	10	78	39	0	0	60	0.97
669543--669578	18	2.0	18	94	0	63	30	22	2	44	1.67
670247--670278	15	2.1	15	94	0	55	59	0	0	40	0.97
670211--670273	26	2.3	26	74	15	65	60	1	3	34	1.22
670247--670279	8	4.2	8	88	7	50	60	0	0	39	0.97
670292--670337	21	2.2	21	88	0	65	21	8	28	41	1.83
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
670425--670465	20	2.0	20	86	9	57	63	0	2	34	1.08
670615--670647	17	1.9	17	93	0	57	27	3	0	69	1.03
670716--670759	22	2.1	20	83	8	52	25	2	4	68	1.20
684315--684446	66	2.0	66	100	0	264	39	9	12	39	1.74
691976--692038	31	2.0	31	96	0	117	41	15	17	25	1.89
698536--698561	13	2.0	13	100	0	52	15	0	23	61	1.33
703432--703479	24	2.0	26	84	12	66	64	2	2	31	1.16
703596--703677	9	8.1	9	82	16	83	31	2	1	64	1.14
703642--703685	9	4.8	9	88	5	52	40	0	0	59	0.98
703644--703685	19	2.3	18	87	4	57	40	0	0	59	0.97

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