genome.fa.s3.2.7.7.80.10.50.1000.36.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  36  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)
9697915--9697951	15	2.6	14	88	12	58	35	0	16	48	1.46
9698177--9698224	25	1.9	25	86	0	69	29	4	20	45	1.70
9698202--9698249	20	2.4	20	73	13	53	39	2	16	41	1.60
9699890--9699924	18	1.9	18	88	0	52	25	14	20	40	1.90
9703849--9703904	18	3.1	17	79	5	58	26	14	16	42	1.86
9707139--9707331	41	4.7	41	74	8	151	37	29	17	15	1.91
9707143--9707331	82	2.3	82	78	8	206	37	29	17	15	1.91
9707196--9707374	82	2.2	81	81	3	198	37	29	17	15	1.91
9713298--9713330	2	16.5	2	93	0	57	48	3	0	48	1.17
9713913--9713945	7	4.7	7	92	7	50	87	3	9	0	0.63
9723710--9723754	22	2.0	23	82	4	56	35	24	15	24	1.94
9734265--9734289	3	8.3	3	100	0	50	32	36	0	32	1.58
9764974--9765012	20	1.9	21	84	5	53	38	0	17	43	1.50
9776258--9776295	19	2.0	20	84	5	51	76	0	13	10	1.02
9779633--9779841	41	5.1	41	87	0	310	37	17	28	16	1.92
9793878--9793946	32	2.2	32	92	2	113	23	7	30	39	1.82
9797907--9797952	22	2.1	22	95	0	83	4	10	21	63	1.44
9799352--9799390	19	2.1	19	85	0	51	33	5	12	48	1.63
9799518--9799542	7	3.6	7	100	0	50	0	12	0	88	0.53
9803050--9803603	138	4.0	138	91	0	871	46	6	8	39	1.59
9803579--9803725	75	2.0	75	90	5	235	31	14	7	46	1.72
9804276--9804308	17	1.9	17	88	11	50	33	6	27	33	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9807281--9807379	30	3.3	30	76	8	85	42	12	24	21	1.86
9818773--9818840	25	2.6	25	81	4	73	23	26	25	25	2.00
9832270--9832322	24	2.3	22	80	6	61	66	9	1	22	1.31
9837092--9837169	40	1.9	41	81	2	95	46	5	1	47	1.33
9837289--9837346	25	2.3	25	87	0	80	55	1	0	43	1.10
9837529--9837576	18	2.8	17	90	6	71	45	2	2	50	1.25
9842842--9842871	3	10.0	3	100	0	60	0	33	0	66	0.92
9849105--9849146	19	2.3	18	84	8	50	42	2	4	50	1.36
9852568--9852630	30	2.1	30	85	8	85	33	1	7	57	1.37
9855145--9855201	21	2.7	22	78	10	66	33	22	21	22	1.97
9855146--9855214	21	3.3	21	77	4	59	33	21	20	24	1.97
9857718--9857773	20	2.7	21	78	13	55	46	12	3	37	1.59
9857738--9857779	21	2.0	22	85	4	59	45	16	4	33	1.69
9864154--9864186	15	2.1	16	94	5	59	27	12	6	54	1.60
9875065--9875106	22	2.0	21	90	4	66	45	0	40	14	1.45
9890799--9890838	21	1.9	21	89	0	62	27	0	20	52	1.46
9895151--9895185	14	2.4	15	90	4	54	11	2	0	85	0.69
9895375--9895399	2	12.5	2	100	0	50	48	0	0	52	1.00
9899833--9899872	6	6.8	6	88	5	64	82	0	17	0	0.67
9901137--9901714	88	6.6	88	89	0	852	27	29	24	19	1.98
9901714--9902172	44	10.7	44	80	7	498	28	17	25	28	1.98
9901714--9902175	126	3.6	126	89	2	685	28	17	25	28	1.98
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
9904045--9904080	12	3.1	11	92	8	54	11	2	0	86	0.68
9904277--9904315	2	19.5	2	100	0	78	48	0	0	51	1.00
9923660--9923697	17	2.2	17	95	0	67	18	26	34	21	1.96
9925175--9925289	44	2.7	43	70	18	103	26	20	26	26	1.99
9927259--9927296	18	2.1	19	90	5	60	15	23	0	60	1.35
9927379--9927417	19	2.1	19	90	0	60	41	17	17	23	1.91
9929316--9929399	43	2.0	43	85	0	114	54	1	20	23	1.51
9930703--9930803	49	2.1	49	90	0	157	44	5	23	25	1.76
9942190--9942222	2	16.5	2	87	12	50	48	0	3	48	1.17
9942365--9942393	11	2.5	12	88	11	51	75	0	24	0	0.80
9944300--9944418	30	4.1	29	88	7	172	29	8	19	42	1.80
9944300--9944419	58	2.1	59	88	4	181	29	8	19	43	1.80
9944569--9944647	41	1.9	42	89	2	124	25	18	25	30	1.98
9958102--9958182	30	2.7	30	80	0	99	28	20	27	23	1.99
9961872--9961921	17	2.8	17	82	8	55	52	0	0	48	1.00
9963575--9963628	21	2.8	19	76	20	51	31	1	3	62	1.23
9964041--9964065	5	5.0	5	100	0	50	60	0	0	40	0.97
9967509--9967534	11	2.4	11	100	0	52	46	0	0	53	1.00
9969960--9969998	20	1.9	21	89	5	62	33	12	10	43	1.77
9996321--9996387	21	3.2	20	75	10	55	53	5	0	40	1.25
9999822--9999846	13	1.9	13	100	0	50	64	0	4	32	1.12
10003156--10003223	35	1.9	35	90	0	109	33	8	25	32	1.86
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10004206--10004244	18	2.2	18	90	9	62	12	5	2	79	1.00
10004874--10004951	3	25.3	3	92	5	129	32	2	0	65	1.06
10005297--10005338	22	2.0	20	86	9	57	35	2	4	57	1.33
10009665--10009728	7	8.9	7	80	14	51	82	9	0	7	0.83
10009666--10009727	14	4.4	14	81	4	61	82	9	0	8	0.85
10009663--10009734	30	2.4	31	84	11	96	81	9	0	8	0.86
10009664--10009734	8	9.4	8	79	14	62	81	9	0	8	0.87
10009665--10009742	22	3.5	22	77	17	65	79	10	1	8	0.99
10009662--10009744	29	2.9	29	84	12	100	78	10	1	9	1.03
10009747--10009786	6	6.3	6	86	11	53	77	0	20	2	0.88
10011857--10012789	88	10.6	88	90	1	1351	27	23	24	24	2.00
10012761--10012880	55	2.2	56	93	1	215	33	16	25	24	1.96
10013014--10013658	50	12.9	50	81	0	698	33	21	19	26	1.97
10013014--10013655	100	6.4	100	93	0	1034	33	21	19	26	1.97
10013547--10013701	50	3.1	49	73	12	127	33	22	19	24	1.97
10013014--10013739	100	7.3	100	91	0	465	33	20	19	26	1.97
10013727--10013776	25	2.0	25	84	0	64	36	20	18	26	1.95
10013977--10014026	25	2.0	25	84	0	64	36	20	18	26	1.95
10013668--10014239	125	4.6	125	97	0	1090	35	19	19	26	1.95
10014323--10014518	44	4.5	43	74	6	153	31	21	21	25	1.98
10015541--10015579	18	2.2	18	90	9	62	10	7	2	79	1.02
10016207--10016231	3	8.3	3	100	0	50	36	0	0	64	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10018799--10018837	18	2.1	19	85	4	53	25	0	15	58	1.37
10019209--10019265	22	2.5	22	81	13	64	43	1	1	52	1.21
10021067--10021097	12	2.6	12	94	0	53	70	3	25	0	1.02
10022186--10022295	37	2.8	38	73	8	87	20	20	26	31	1.98
10031304--10031343	3	13.3	3	94	0	71	0	2	32	65	1.06
10031363--10031387	6	4.2	6	100	0	50	16	0	52	32	1.44
10031562--10031604	3	14.3	3	85	0	59	0	4	30	65	1.13
10034660--10034904	50	4.8	50	79	3	213	23	28	20	27	1.99
10039122--10039171	26	1.9	26	95	0	91	46	10	12	32	1.74
10044386--10044419	16	2.1	16	88	0	50	29	11	23	35	1.90
10044455--10044506	25	2.0	26	88	3	79	42	9	5	42	1.61
10044627--10044664	16	2.4	16	100	0	76	50	5	5	39	1.48
10054133--10054278	75	1.9	75	87	2	213	29	18	23	28	1.98
10057154--10057222	31	2.2	31	92	0	111	36	10	8	44	1.69
10057446--10057791	43	8.1	43	82	3	369	29	21	19	29	1.98
10058065--10058104	21	2.0	19	90	9	62	7	42	10	40	1.67
10063163--10063467	9	32.6	9	74	13	224	35	0	19	43	1.56
10063127--10063467	56	6.0	56	91	3	502	36	0	18	44	1.56
10063127--10063467	114	3.0	112	90	3	529	36	0	18	44	1.56
10063127--10063467	170	2.0	172	91	1	551	36	0	18	44	1.56
10069115--10069235	41	3.0	41	92	0	197	24	25	20	28	1.99
10070008--10070062	2	28.0	2	76	10	51	43	5	3	47	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10075264--10075319	28	2.0	28	100	0	112	39	17	14	28	1.89
10080566--10080607	16	2.7	15	79	13	50	28	0	9	61	1.27
10083681--10083754	25	3.2	25	60	25	63	22	14	6	55	1.63
10083682--10083768	43	2.0	43	100	0	174	25	13	6	54	1.64
10085603--10085646	16	2.8	16	80	13	54	18	4	4	72	1.19
10087227--10087288	30	2.1	30	100	0	124	24	16	32	27	1.96
10088696--10088897	29	7.0	29	81	4	228	25	15	22	36	1.93
10095460--10095533	36	2.1	36	84	5	96	37	18	18	24	1.94
10095524--10095556	16	2.1	16	100	0	66	36	6	24	33	1.80
10102043--10102078	18	2.0	18	100	0	72	55	16	16	11	1.68

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