genome.fa.s3.2.7.7.80.10.50.1000.13.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  13  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)
3708240--3708270	12	2.6	12	100	0	62	32	61	6	0	1.21
3708210--3708270	24	2.5	24	81	0	68	31	60	6	1	1.32
3708198--3708382	75	2.5	75	84	0	190	28	51	6	13	1.65
3709716--3709785	20	3.3	20	67	21	61	22	24	15	37	1.93
3709715--3709802	44	2.0	44	100	0	176	22	22	15	38	1.92
3709726--3709793	20	3.2	20	66	22	57	22	22	19	36	1.95
3713940--3713976	14	2.6	14	86	0	56	18	2	10	67	1.32
3714236--3714273	18	2.1	18	85	9	51	28	2	7	60	1.38
3716956--3717163	98	2.1	97	83	7	251	35	14	15	33	1.89
3717123--3717318	106	1.8	107	91	1	322	40	15	17	27	1.89
3717123--3717318	107	1.8	105	91	5	322	40	15	17	27	1.89
3718508--3718554	22	2.3	20	86	13	62	23	12	10	53	1.70
3724230--3724267	3	12.7	3	100	0	76	68	0	0	31	0.90
3726890--3726947	19	3.2	19	80	9	68	34	3	3	58	1.32
3733749--3733930	44	4.2	43	68	17	117	25	18	24	31	1.97
3733977--3734733	132	5.8	132	93	1	1241	26	17	24	30	1.97
3734087--3734675	44	13.5	43	65	16	191	26	18	25	30	1.98
3733977--3734733	263	2.9	264	93	1	1243	26	17	24	30	1.97
3740750--3740800	9	5.7	9	75	9	50	25	0	0	74	0.82
3740749--3740857	10	10.5	10	74	16	71	28	0	0	70	0.93
3740751--3740810	17	3.4	17	80	13	75	26	0	0	73	0.84
3740761--3740858	48	2.1	47	85	10	132	29	1	0	69	0.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3740820--3740881	32	1.9	32	83	0	79	32	1	3	62	1.20
3741073--3741112	16	2.5	16	100	0	80	45	7	17	30	1.76
3742883--3742965	39	2.2	39	88	2	123	19	19	21	39	1.92
3742883--3743049	45	4.0	39	77	17	147	19	18	21	40	1.92
3742910--3743064	45	3.4	45	91	0	247	19	18	20	41	1.91
3743489--3743535	22	2.1	22	96	0	85	61	6	14	17	1.53
3746253--3746289	2	18.5	2	94	0	65	51	0	0	48	1.00
3753819--3753905	3	29.0	3	88	0	129	60	3	1	34	1.21
3754996--3755057	5	13.2	5	78	13	69	61	1	0	37	1.06
3754995--3755057	17	3.8	17	78	21	55	60	1	0	38	1.07
3754995--3755055	22	2.9	21	81	11	63	59	1	0	39	1.08
3755011--3755055	22	2.0	22	91	8	72	57	0	0	42	0.98
3754990--3755057	34	2.1	31	83	8	82	58	1	0	39	1.07
3755011--3755056	24	1.9	24	86	8	67	58	0	0	41	0.98
3759744--3759793	3	16.7	3	100	0	100	34	0	0	66	0.92
3759868--3759962	44	2.2	44	96	0	172	41	12	22	24	1.88
3759870--3759976	44	2.4	44	90	0	142	39	14	23	23	1.91
3761268--3761330	29	2.2	29	94	0	108	39	0	11	49	1.38
3763155--3763205	20	2.5	20	80	0	66	11	35	19	33	1.88
3763801--3763889	3	29.7	3	100	0	178	66	0	0	33	0.92
3764125--3764157	10	3.7	9	88	12	50	27	12	0	60	1.32
3765910--3765953	12	3.8	12	90	3	72	54	0	4	40	1.21
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3765900--3766029	12	11.9	11	75	18	71	56	0	3	40	1.15
3765954--3766035	30	2.9	27	84	15	87	58	0	2	39	1.11
3765973--3766029	11	5.5	11	76	21	61	54	0	3	42	1.17
3765981--3766018	19	2.1	19	95	5	69	55	0	2	42	1.14
3765900--3766019	46	2.7	44	78	13	138	56	0	3	40	1.16
3765967--3766036	30	2.5	28	90	9	115	57	0	2	40	1.14
3767426--3767461	4	8.8	4	87	6	54	0	22	2	75	0.94
3767425--3767460	13	2.8	13	91	4	56	0	22	2	75	0.94
3771824--3771863	21	2.0	20	90	5	62	60	12	0	27	1.33
3786585--3786609	11	2.3	11	100	0	50	16	0	20	64	1.30
3792790--3792939	41	3.7	41	91	0	237	24	28	18	28	1.98
3792789--3792988	82	2.4	82	82	6	237	25	27	18	30	1.98
3799521--3799546	4	6.5	4	100	0	52	26	0	0	73	0.84
3800681--3800779	41	2.4	41	91	1	155	24	25	11	39	1.88
3807708--3808030	36	8.7	36	67	9	130	23	20	23	32	1.98
3807742--3807953	40	5.6	39	67	10	136	22	18	24	34	1.96
3807708--3808047	76	4.6	74	84	4	366	22	19	23	33	1.97
3808109--3808166	24	2.4	24	91	2	89	50	3	27	18	1.63
3808458--3808525	30	2.2	31	84	2	84	48	7	17	26	1.73
3813378--3813403	13	2.0	13	100	0	52	15	38	0	46	1.46
3814408--3814498	47	1.9	47	95	0	164	36	6	14	42	1.71
3815583--3815616	15	2.3	15	89	0	50	5	11	11	70	1.32
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3815786--3815811	11	2.4	11	100	0	52	7	0	0	92	0.39
3824947--3824978	9	3.6	9	91	0	55	12	0	0	87	0.54
3824945--3824985	8	5.0	8	83	16	57	14	0	0	85	0.60
3824948--3824985	16	2.4	16	95	0	67	13	0	0	86	0.56
3824949--3825011	23	2.7	23	76	9	65	12	6	1	79	0.99
3825795--3825851	30	1.9	30	88	0	87	19	36	29	14	1.91
3833683--3833727	18	2.4	19	85	11	65	8	8	2	80	1.00
3835358--3835411	6	9.0	6	80	8	65	14	1	5	77	1.03
3839663--3839687	12	2.1	12	100	0	50	56	0	8	36	1.29
3844028--3844269	121	2.0	121	91	1	396	35	12	28	23	1.91
3845181--3845248	4	16.5	4	76	19	61	22	4	0	73	1.01
3845185--3845248	21	3.0	21	76	15	69	21	4	0	73	1.01
3846091--3846283	102	1.9	102	81	10	234	29	14	25	31	1.95
3846268--3846307	17	2.4	17	91	4	64	82	0	0	17	0.67
3846268--3846310	8	5.5	8	78	15	54	81	0	0	18	0.69
3846271--3846310	14	2.7	15	92	7	64	82	0	0	17	0.67
3846859--3846893	15	2.4	15	90	4	54	48	0	8	42	1.33
3848492--3848518	6	4.5	6	100	0	54	14	14	0	70	1.17
3849032--3849074	8	5.1	8	78	10	50	20	0	2	76	0.89
3849120--3849154	11	3.2	11	100	0	70	25	0	8	65	1.21
3849769--3849815	23	2.0	23	84	8	60	6	23	2	68	1.24
3850475--3850539	29	2.3	28	76	5	69	21	20	18	40	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3850896--3851328	123	3.5	123	89	5	655	30	17	22	29	1.97
3851508--3851553	21	2.2	21	96	0	83	23	2	30	43	1.66
3852095--3852137	18	2.4	19	84	7	54	39	9	30	20	1.84
3853984--3854049	11	5.9	11	75	13	64	48	1	25	24	1.60
3853986--3854039	22	2.5	22	84	3	74	48	1	25	24	1.61
3854581--3854623	18	2.4	18	88	0	59	25	9	25	39	1.85
3855239--3855319	31	2.7	29	74	14	85	51	16	13	18	1.76
3855841--3855881	14	2.9	15	78	7	50	75	0	19	4	0.98
3860410--3860434	3	8.3	3	100	0	50	0	32	0	68	0.90
3863493--3863873	190	2.0	190	88	1	566	34	21	13	30	1.92
3867968--3868011	2	22.0	2	100	0	88	50	0	0	50	1.00
3868370--3868409	3	13.3	3	89	10	64	65	0	0	35	0.93
3868369--3868409	21	2.0	21	95	4	75	63	0	0	36	0.95
3868370--3868425	24	2.4	24	85	8	71	66	1	0	32	1.03
3868629--3868667	19	2.0	21	85	10	55	69	5	10	15	1.34
3868691--3868794	51	2.0	53	94	3	185	15	21	3	59	1.52
3868764--3868796	13	2.5	13	86	13	50	3	9	0	87	0.63
3868925--3869021	21	4.7	21	91	5	153	38	11	9	41	1.73
3868902--3869016	21	5.5	20	86	6	124	39	13	8	39	1.75
3869890--3870206	48	6.6	48	78	7	259	34	19	23	22	1.97
3869936--3870208	95	2.9	95	80	8	297	34	19	24	21	1.96
3869936--3870215	143	2.0	143	83	4	359	35	19	23	21	1.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
3875507--3875689	48	3.7	49	83	3	224	38	25	19	16	1.93
3875507--3876198	50	13.6	51	74	9	479	34	23	18	23	1.96
3875507--3875804	101	2.9	100	82	5	271	35	22	18	23	1.95
3875506--3876194	49	13.6	50	73	8	380	33	23	18	23	1.97
3875737--3876100	152	2.4	152	78	5	380	35	23	17	23	1.95
3875829--3876151	102	3.2	101	77	6	264	36	23	17	22	1.95
3877748--3877789	22	2.0	21	86	13	61	64	0	2	33	1.07
3878462--3878646	100	1.8	101	88	5	286	32	22	10	33	1.89
3879011--3879061	20	2.5	20	93	0	84	31	19	13	35	1.91
3879147--3879216	28	2.5	27	84	11	79	60	1	2	35	1.21

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