genome.fa.s16.2.7.7.80.10.50.1000.2.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: D03
Parameters: 2 7 7 80 10 50 1000
Length:  53248092

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   

This is table  2  of  175  ( 20966 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)
367221--367273	16	3.4	17	73	21	53	56	0	0	43	0.99
367147--367333	60	3.1	59	66	13	157	49	6	2	41	1.42
367099--367390	119	2.4	120	93	2	489	50	4	2	42	1.35
376944--377125	21	8.7	21	77	2	87	21	8	44	24	1.81
376944--377109	42	4.0	42	77	6	147	22	7	44	25	1.79
377112--377242	21	6.2	21	87	0	136	22	11	39	25	1.88
377289--377428	42	3.3	43	87	2	169	25	15	40	18	1.90
377334--377431	21	4.7	21	84	0	124	28	17	38	15	1.90
377351--377455	21	5.0	21	84	0	120	28	15	40	16	1.88
377334--377455	42	2.9	42	87	2	138	27	16	39	16	1.90
386371--386436	29	2.2	31	83	5	82	59	3	6	31	1.37
396850--396918	31	2.2	31	87	5	95	43	10	18	27	1.82
396800--396987	89	2.1	90	83	4	229	43	13	18	25	1.86
397007--397056	14	3.6	14	81	8	57	28	4	0	68	1.08
397007--397044	13	2.7	14	88	8	51	26	5	0	68	1.11
397730--397772	18	2.4	18	88	7	61	48	0	0	51	1.00
401568--401597	2	15.0	2	100	0	60	50	50	0	0	1.00
402612--402652	5	8.0	5	86	2	55	75	21	2	0	0.92
408832--408894	13	4.5	13	76	18	56	61	3	3	31	1.27
410490--410579	26	3.5	26	72	15	80	34	1	0	64	1.01
410538--410591	26	2.0	26	85	10	72	33	0	1	64	1.04
413785--413849	28	2.4	28	92	2	105	41	7	1	49	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
414075--414124	15	3.1	15	80	8	55	44	16	0	40	1.47
414768--414826	27	2.2	27	93	0	100	49	0	8	42	1.33
416136--416180	21	2.1	21	100	0	90	60	8	0	31	1.28
416653--416706	26	2.1	26	89	0	81	70	5	0	24	1.08
416676--416730	15	3.8	15	76	9	60	76	0	0	23	0.79
416663--416725	26	2.3	26	89	10	92	73	0	0	26	0.84
419088--419125	18	2.1	18	90	0	58	34	7	23	34	1.84
420476--420510	18	2.0	17	88	5	52	45	0	0	54	0.99
420596--420644	18	2.9	17	82	8	55	46	0	2	51	1.12
425476--425517	18	2.4	18	76	4	50	66	2	7	23	1.28
426103--426164	18	3.3	20	77	18	64	41	1	3	53	1.27
428040--428079	11	3.6	12	83	16	59	27	0	5	67	1.11
431562--431589	6	4.7	6	100	0	56	50	0	0	50	1.00
432532--432570	17	2.2	18	86	4	53	58	0	7	33	1.26
441586--441620	13	2.7	13	100	0	70	0	31	25	42	1.55
447733--447761	7	4.1	7	100	0	58	41	0	0	58	0.98
448237--448276	16	2.5	16	91	0	62	37	10	25	27	1.88
448559--448613	28	2.0	28	85	7	76	58	0	1	40	1.09
448576--448611	18	2.1	18	94	5	65	63	0	0	36	0.94
451652--451682	15	2.1	15	93	0	53	41	19	6	32	1.77
452133--452201	23	3.1	23	73	23	67	55	1	1	42	1.18
453759--454001	50	4.8	50	88	0	351	20	30	23	25	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
456551--456663	60	1.9	58	87	5	165	51	11	14	23	1.74
465113--465189	32	2.4	32	86	4	102	19	18	22	40	1.92
467459--467488	8	3.8	8	100	0	60	33	13	13	40	1.83
486525--486558	16	2.1	16	88	0	50	79	0	0	20	0.73
490471--490616	72	2.0	72	94	0	256	37	25	16	20	1.93
495033--495090	29	2.0	29	93	0	98	31	5	36	27	1.79
495640--495674	11	3.1	12	88	12	56	34	0	0	65	0.93
495797--495858	30	2.1	30	93	0	106	59	12	3	24	1.48
498009--498227	118	1.8	119	92	4	370	40	19	10	29	1.86
503883--503934	24	2.2	24	85	0	68	51	7	5	34	1.54
507024--507063	18	2.1	18	90	9	62	57	0	0	42	0.98
510782--510823	19	2.2	20	86	4	59	35	0	2	61	1.09
511330--511372	9	4.8	9	94	0	77	23	9	30	37	1.86
517490--517558	16	4.2	16	92	3	120	24	1	37	36	1.65
517490--517558	33	2.1	32	94	2	120	24	1	37	36	1.65
517544--517628	44	1.9	45	85	2	118	29	7	27	36	1.83
517794--517828	18	2.0	17	88	5	52	54	0	0	45	0.99
517777--518751	120	8.1	120	99	0	1869	47	6	2	43	1.40
518740--519425	120	5.7	120	99	0	1345	47	6	1	43	1.40
518314--519177	426	2.0	426	99	0	1710	47	6	1	43	1.40
518074--519417	666	2.0	666	98	0	2625	47	6	2	43	1.41
518194--519297	546	2.0	546	99	0	2163	47	6	1	43	1.41
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
524378--524466	45	2.0	44	86	6	126	37	1	15	46	1.54
524481--524528	24	2.0	25	87	4	71	39	6	4	50	1.47
524772--524817	23	2.0	23	100	0	92	39	17	21	21	1.93
525484--525559	39	1.9	39	86	0	107	31	10	18	39	1.85
528513--528579	22	3.0	22	79	16	68	29	4	0	65	1.12
528532--528570	14	2.9	14	84	3	53	33	0	0	66	0.92
529423--529575	58	2.6	58	88	0	225	37	20	9	33	1.84
533586--533610	3	8.3	3	100	0	50	32	0	0	68	0.90
533647--533679	15	2.1	16	88	5	50	48	3	12	36	1.56
534731--534798	29	2.3	29	80	9	77	39	4	7	48	1.51
534731--534798	28	2.3	29	80	9	77	39	4	7	48	1.51
535096--535151	29	1.9	29	85	0	76	37	5	8	48	1.58
540616--540656	21	2.0	21	90	0	64	19	29	21	29	1.98
544834--544890	4	14.2	4	100	0	114	26	0	24	49	1.51
548073--548100	7	4.0	7	100	0	56	85	0	14	0	0.59
553933--554791	278	3.0	282	80	7	728	27	16	18	37	1.92
554817--554879	21	3.0	22	80	17	71	65	1	33	0	1.03
556663--557012	126	2.8	126	84	2	463	31	13	20	34	1.92
560088--560546	23	19.7	23	74	16	358	28	1	24	45	1.63
560079--560146	29	2.3	29	92	0	109	27	1	26	44	1.63
560121--560469	67	5.1	67	84	7	445	29	1	22	46	1.60
560345--560453	22	4.6	22	76	19	96	26	0	22	50	1.49
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
560262--560520	50	5.5	49	80	11	269	27	1	23	47	1.61
560565--560690	52	2.7	43	75	21	126	52	7	0	40	1.29
560583--560699	53	2.2	53	92	3	193	54	7	0	37	1.29
561071--561105	18	1.9	18	94	0	61	34	8	31	25	1.86
561758--561782	7	3.6	7	100	0	50	60	12	0	28	1.32
563012--563085	22	3.4	22	80	9	80	45	0	29	24	1.53
562925--563040	51	2.3	51	92	0	187	47	0	24	28	1.52
565879--566073	102	1.9	103	89	1	302	28	27	16	27	1.97
571804--571880	30	2.5	30	87	8	111	45	1	2	50	1.23
573218--573254	18	2.1	18	100	0	74	27	16	10	45	1.80
573824--573849	10	2.6	10	100	0	52	34	0	0	65	0.93
575442--575512	31	2.2	32	85	5	99	33	11	11	43	1.76
577316--577369	4	13.5	4	100	0	108	24	0	25	50	1.50
588036--588060	13	1.9	13	100	0	50	0	92	0	8	0.40
589016--589373	146	2.5	145	89	3	533	39	18	16	25	1.91
596073--596098	7	3.7	7	100	0	52	30	0	42	26	1.56
596253--596293	20	2.0	20	100	0	82	24	14	14	46	1.82
596254--596298	20	2.5	17	86	13	56	26	15	15	42	1.87
596460--596518	29	2.0	29	100	0	118	33	16	16	32	1.92
599682--599741	18	3.3	18	86	6	68	80	3	13	3	0.97
600541--600711	66	2.6	65	84	1	207	29	17	30	22	1.97
603782--603837	29	1.9	29	92	0	94	35	14	7	42	1.73
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
604122--604161	20	2.0	20	85	9	55	67	2	2	27	1.16
622255--622870	164	3.7	164	87	3	819	26	20	17	34	1.95
627462--627552	37	2.7	33	75	17	87	39	3	0	57	1.15
633458--633551	47	2.0	46	89	6	145	36	12	9	41	1.76
633844--633878	18	1.9	18	100	0	70	71	17	0	11	1.14
634179--634579	198	2.0	198	96	0	730	30	19	13	36	1.90
638878--638911	18	2.0	17	88	11	52	29	2	5	61	1.34
639010--639061	16	3.3	15	81	10	52	57	0	0	42	0.98
639010--639058	22	2.2	22	85	10	64	59	0	0	40	0.98
646013--646054	15	2.5	17	74	18	52	69	0	0	30	0.89

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