genome.fa.s3.2.7.7.80.10.50.1000.2.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: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  45765648

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   

This is table  2  of  150  ( 17918 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)
378159--378190	8	3.9	8	95	4	55	87	3	9	0	0.64
378351--378443	29	3.1	29	65	14	71	31	10	17	40	1.83
379812--379851	16	2.5	17	84	15	50	42	10	20	27	1.83
380076--380198	18	6.9	18	66	15	76	53	4	1	40	1.29
380078--380247	89	1.9	89	96	1	315	50	5	1	42	1.35
383253--383283	15	2.1	15	93	0	53	41	19	6	32	1.77
384100--384168	23	3.1	23	73	23	67	56	1	0	42	1.08
384944--385004	27	2.4	25	83	8	79	39	11	1	47	1.50
385374--385411	20	1.9	20	88	0	58	44	7	7	39	1.63
387870--388110	50	4.7	50	84	5	277	20	27	23	28	1.99
387861--388110	100	2.4	104	86	5	328	21	27	23	27	1.99
387917--388110	106	1.9	100	89	6	271	20	28	23	27	1.99
389835--389896	27	2.3	27	81	10	90	14	37	19	29	1.91
389897--389928	16	1.9	17	93	6	57	6	6	18	68	1.32
390632--390741	57	1.9	56	83	9	141	52	12	14	20	1.73
393685--393722	15	2.5	15	83	12	51	44	0	2	52	1.14
394183--394261	31	2.5	31	78	6	97	41	21	11	25	1.86
399281--399346	32	2.1	32	88	5	98	19	18	24	37	1.93
410066--410105	2	20.0	2	89	0	62	47	2	2	47	1.29
417400--417456	28	2.0	28	100	0	114	42	14	7	36	1.72
423585--423728	72	2.0	72	95	0	261	38	25	16	20	1.93
426761--426786	3	8.7	3	100	0	52	34	0	0	65	0.93
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
428924--428988	32	2.1	31	88	5	96	60	13	3	23	1.48
434857--434918	27	2.3	27	88	0	97	30	20	32	16	1.95
435080--435122	21	2.1	21	91	4	70	69	0	2	27	1.00
435389--435426	19	2.0	19	89	0	58	50	7	5	36	1.54
435525--435596	27	2.7	27	93	0	117	52	12	0	34	1.39
435636--435807	27	7.1	24	72	24	148	32	1	13	52	1.48
435639--435810	49	3.6	49	85	6	235	31	1	13	53	1.47
435808--435880	22	3.4	21	67	19	53	34	1	12	52	1.48
436105--436181	27	2.9	28	90	3	115	19	38	24	16	1.92
436220--436276	29	1.9	30	82	3	71	49	3	1	45	1.29
437756--437833	39	1.9	42	82	10	99	48	2	5	43	1.38
438825--438877	24	2.2	24	82	0	61	52	9	5	32	1.57
439491--439532	13	3.2	13	83	12	52	23	7	28	40	1.81
442443--442505	18	3.3	20	91	4	78	61	0	0	38	0.96
442451--442509	18	3.1	19	92	7	102	62	0	0	37	0.95
444784--444859	9	8.4	9	92	0	125	44	22	7	25	1.79
446394--446435	19	2.2	20	86	4	59	35	0	2	61	1.09
448824--449475	329	2.0	329	99	0	1286	33	13	8	43	1.75
452616--452694	39	2.0	39	95	0	140	32	11	18	36	1.87
457534--457564	4	7.8	4	100	0	62	25	0	25	48	1.52
459610--459644	3	11.7	3	100	0	70	31	0	0	68	0.90
461021--461054	2	17.0	2	100	0	68	50	0	0	50	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
466991--467047	4	14.2	4	100	0	114	26	0	24	49	1.51
468762--468849	33	2.5	37	73	19	87	64	6	0	28	1.19
470568--470601	13	2.6	13	95	0	59	38	17	2	41	1.65
473987--474847	280	3.0	282	80	7	732	26	16	18	37	1.92
474873--474935	21	3.0	22	80	17	71	65	1	33	0	1.03
476672--477023	126	2.8	125	86	3	451	30	14	20	33	1.93
480164--480499	23	14.7	23	80	11	361	27	1	25	45	1.64
480165--480473	44	6.8	44	81	12	333	27	1	25	45	1.62
480194--480473	67	4.2	67	83	9	333	27	1	24	46	1.63
480194--480473	90	3.1	90	85	9	335	27	1	24	46	1.63
480195--480499	158	1.9	156	88	4	452	27	1	24	45	1.64
480518--480644	53	2.7	44	77	19	146	51	9	0	39	1.35
480536--480653	53	2.2	53	96	1	220	53	9	0	37	1.33
482912--483034	51	2.4	51	91	1	203	45	0	26	28	1.54
485930--486130	102	2.0	101	90	1	312	29	27	16	26	1.97
491876--491942	30	2.2	31	84	7	84	41	2	4	50	1.37
493261--493327	34	1.9	35	90	3	109	44	13	8	32	1.75
496025--496095	31	2.2	32	85	9	101	32	14	11	42	1.81
497945--497990	4	11.8	4	95	4	85	26	0	26	47	1.52
509536--509890	146	2.4	145	92	1	570	39	18	17	24	1.92
512644--512672	2	14.5	2	100	0	58	51	0	0	48	1.00
516735--516775	20	2.0	20	100	0	82	24	14	14	46	1.82
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
516736--516780	20	2.5	17	86	13	56	26	15	15	42	1.87
516943--517001	29	2.0	29	100	0	118	33	16	16	32	1.92
520170--520217	13	3.4	14	83	13	55	79	6	12	2	1.01
520182--520225	17	2.5	17	85	7	52	79	4	11	4	1.02
521025--521195	66	2.6	65	84	1	207	29	17	30	22	1.97
524293--524348	29	1.9	29	92	0	94	35	14	7	42	1.73
526133--526278	76	1.9	76	85	4	204	29	12	8	49	1.71
527307--527357	24	2.1	24	96	0	93	45	25	13	15	1.83
532473--532648	95	1.9	95	95	0	316	28	17	21	33	1.95
537743--538135	174	2.3	170	86	6	533	35	20	18	25	1.95
543948--544563	164	3.7	164	88	2	844	26	20	18	34	1.95
549179--549249	28	2.4	29	81	13	83	43	4	0	52	1.20
549179--549266	32	3.0	27	74	19	79	43	3	0	53	1.17
549873--549916	11	4.2	11	82	11	56	18	4	27	50	1.66
549886--549960	9	8.2	9	79	8	71	24	9	25	41	1.84
549878--549962	20	4.5	20	76	8	81	23	8	25	42	1.82
555214--555307	47	2.0	46	87	2	134	39	13	6	40	1.71
558727--558764	2	19.0	2	100	0	76	50	0	0	50	1.00
560547--560587	14	2.8	15	79	13	50	58	0	0	41	0.98
561058--561131	30	2.4	31	80	11	80	60	2	4	32	1.29
565360--565403	17	2.6	17	82	13	63	29	2	11	56	1.46
568542--568582	15	2.6	16	75	25	50	68	0	0	31	0.90
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
569362--569390	13	2.2	13	100	0	58	24	0	0	75	0.80
570269--570298	11	2.7	11	89	0	51	63	10	6	20	1.47
575291--575454	8	20.5	8	98	0	247	18	0	31	50	1.47
575647--575686	4	10.0	4	86	0	53	20	2	27	50	1.61
582516--582557	21	2.0	21	100	0	84	47	9	23	19	1.78
585554--585589	2	18.0	2	100	0	72	50	0	0	50	1.00
590251--590307	21	2.8	19	82	15	62	35	40	12	12	1.80
590458--590514	21	2.8	19	82	15	62	35	40	12	12	1.80
590242--590658	207	2.0	206	96	0	762	35	24	14	25	1.93
596993--597024	3	10.7	3	100	0	64	34	31	0	34	1.58
616302--616343	22	2.0	21	85	4	57	47	7	0	45	1.30
629200--629230	6	5.2	6	92	0	53	16	64	16	3	1.42
634023--634048	3	8.7	3	100	0	52	34	65	0	0	0.93
635408--635865	139	3.2	141	86	4	604	27	16	21	33	1.95
635408--635899	144	3.5	142	84	5	613	27	15	21	35	1.94
637683--637763	4	20.8	4	86	5	76	19	3	29	46	1.67
640378--640428	22	2.3	21	80	12	57	45	1	0	52	1.12
646112--646359	138	1.8	136	80	8	297	37	7	18	35	1.80
652690--652731	21	2.0	22	85	4	59	57	4	0	38	1.20
652869--652930	30	2.1	30	93	3	108	50	1	0	48	1.10
655233--655258	11	2.4	11	100	0	52	92	7	0	0	0.39
655632--655664	2	16.5	2	100	0	66	0	0	48	51	1.00
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
668916--669190	137	2.0	138	95	0	498	26	11	21	41	1.86
669047--669398	160	2.2	159	90	1	560	26	10	21	41	1.86
670395--670429	17	2.0	18	94	5	63	45	5	8	40	1.58
671428--671559	31	4.4	31	70	5	99	20	18	19	41	1.90
671755--671852	31	3.2	31	88	1	126	43	20	14	21	1.87
685250--685684	166	2.6	165	87	3	597	31	18	17	33	1.94
687570--687608	2	19.5	2	89	0	60	48	2	2	46	1.29
691640--691668	3	9.7	3	100	0	58	34	34	0	31	1.58
691884--692405	283	1.9	278	84	10	704	20	12	16	49	1.79
693728--693830	51	2.0	52	88	1	154	35	17	14	32	1.90

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