genome.fa.s3.2.7.7.80.10.50.1000.37.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  37  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)
10104189--10104310	62	2.0	62	98	0	235	35	11	22	30	1.90
10119881--10119922	21	2.0	21	100	0	84	19	4	14	61	1.49
10120693--10120717	5	5.0	5	100	0	50	20	0	0	80	0.72
10125991--10126330	30	11.4	30	80	8	200	37	11	25	25	1.90
10125991--10126330	60	5.7	60	76	7	271	37	11	25	25	1.90
10125991--10126300	90	3.5	89	76	4	270	38	11	24	25	1.89
10126110--10126270	29	5.4	29	80	7	164	39	12	26	21	1.89
10134883--10134920	18	2.1	18	100	0	76	39	10	10	39	1.74
10135443--10135866	209	2.0	208	98	0	821	25	12	14	46	1.80
10137033--10137082	25	2.0	25	96	0	91	26	20	12	42	1.86
10143140--10143202	17	3.5	17	69	12	54	49	14	3	33	1.59
10143398--10143432	13	2.8	13	91	4	54	11	2	48	37	1.54
10153109--10153304	67	2.9	67	87	3	281	29	14	18	37	1.91
10153244--10153365	58	2.1	58	84	6	158	28	13	15	41	1.86
10157275--10157306	12	2.7	12	95	0	55	50	0	12	37	1.41
10157672--10157841	45	3.8	45	80	1	153	43	11	20	24	1.84
10160593--10160646	19	2.9	19	86	8	67	38	1	7	51	1.41
10160593--10160636	18	2.5	17	82	10	52	40	2	6	50	1.42
10160598--10160668	20	3.7	20	83	9	76	33	1	9	54	1.42
10160596--10160668	19	3.9	20	79	12	66	35	1	9	53	1.42
10163300--10163388	33	2.7	33	84	6	117	28	12	32	26	1.92
10164806--10164859	20	2.8	20	88	2	74	27	0	3	68	1.06
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10165293--10165331	14	2.7	15	88	8	62	38	0	0	61	0.96
10170028--10170143	42	2.8	42	84	5	128	18	17	16	48	1.82
10170032--10170164	21	6.3	21	74	6	99	17	17	15	49	1.80
10172779--10173138	8	45.0	8	97	0	594	25	3	25	46	1.67
10183844--10183892	22	2.3	22	85	3	64	30	4	40	24	1.74
10184006--10184031	11	2.4	11	100	0	52	0	0	7	92	0.39
10186854--10186900	24	2.0	24	87	4	69	68	6	0	25	1.13
10186859--10186892	17	1.9	18	94	5	61	70	5	0	23	1.09
10186854--10186901	23	2.0	23	88	8	69	68	6	0	25	1.12
10189893--10189935	22	2.0	22	95	0	77	20	16	34	27	1.94
10189894--10189942	22	2.2	22	88	0	71	24	20	28	26	1.99
10190799--10190841	2	21.5	2	100	0	86	51	0	0	48	1.00
10191003--10191032	13	2.3	13	100	0	60	43	10	16	30	1.81
10193630--10193728	29	3.5	29	79	14	109	45	19	16	19	1.86
10193630--10193719	28	3.1	28	80	9	101	44	18	16	20	1.87
10195490--10195581	43	2.2	43	96	2	168	25	4	20	50	1.67
10196270--10196304	17	2.1	17	100	0	70	42	11	5	40	1.65
10201165--10201262	17	5.4	17	66	13	61	32	3	14	50	1.58
10201181--10201271	17	4.9	19	69	14	64	34	4	14	47	1.64
10201160--10201271	37	3.0	37	92	0	179	33	4	14	47	1.64
10201269--10201349	9	8.6	9	84	10	108	22	7	29	40	1.81
10201269--10201349	20	4.3	18	87	6	108	22	7	29	40	1.81
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10201269--10201352	29	2.9	29	89	10	136	21	7	28	42	1.79
10201412--10201472	28	2.2	28	88	2	88	40	8	16	34	1.78
10201774--10202014	127	1.9	126	80	6	278	46	7	8	37	1.63
10202504--10202563	30	2.0	31	83	3	77	21	35	0	43	1.53
10203171--10203196	5	5.2	5	100	0	52	19	19	19	42	1.90
10206420--10206515	46	2.1	45	82	3	120	37	2	15	44	1.58
10207429--10207470	21	2.0	21	85	0	57	35	0	26	38	1.57
10207848--10207975	64	2.0	64	79	0	139	25	19	21	33	1.97
10209801--10209923	42	2.9	42	77	7	124	18	21	17	43	1.89
10212706--10212787	4	20.8	4	73	14	55	4	21	1	71	1.11
10212713--10212780	25	2.7	25	82	8	77	4	22	1	72	1.11
10212796--10212844	26	1.9	25	87	4	71	36	4	0	59	1.17
10212818--10212901	38	2.2	38	79	8	91	51	3	1	44	1.26
10216872--10216932	2	30.0	2	79	9	61	45	4	0	49	1.23
10217096--10217181	4	20.5	4	73	13	66	20	4	4	69	1.25
10217307--10217625	108	3.0	108	87	1	453	30	16	18	34	1.93
10218801--10218846	24	1.9	24	82	8	58	54	10	0	34	1.36
10222606--10222740	65	2.1	64	80	4	155	48	6	9	34	1.62
10230846--10230870	13	1.9	13	100	0	50	56	20	0	24	1.43
10232198--10232250	5	10.8	5	95	4	99	58	0	0	41	0.98
10253478--10253510	11	2.8	12	86	4	50	33	3	12	51	1.54
10256435--10256481	19	2.5	20	86	6	62	59	8	2	29	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10258896--10258949	26	2.1	26	96	0	99	24	22	29	24	1.99
10258855--10258985	67	1.9	68	84	4	176	25	18	27	28	1.98
10258922--10259070	42	3.6	41	80	7	156	22	16	25	34	1.95
10263545--10263573	13	2.2	13	100	0	58	41	0	0	58	0.98
10263853--10263990	30	4.5	31	73	9	113	43	4	11	40	1.61
10263853--10263999	61	2.4	62	81	3	163	42	4	12	40	1.63
10264676--10264702	2	13.5	2	100	0	54	48	0	0	51	1.00
10270043--10270082	21	1.9	21	85	10	55	35	2	0	62	1.09
10270110--10270165	25	2.1	27	84	12	73	42	0	0	57	0.99
10270135--10270170	16	2.1	18	90	10	58	41	0	0	58	0.98
10280239--10280277	20	2.0	20	90	10	62	10	10	0	79	0.94
10282139--10282174	15	2.3	16	85	4	56	41	0	0	58	0.98
10282152--10282182	10	3.1	10	95	0	53	41	0	0	58	0.98
10282357--10282399	16	2.7	16	96	0	77	39	4	37	18	1.72
10282334--10282472	69	2.0	69	90	0	215	31	8	31	28	1.87
10282426--10282464	16	2.4	16	86	0	51	38	2	33	25	1.70
10282439--10282474	16	2.2	16	95	0	63	41	0	30	27	1.56
10282688--10282729	15	2.7	16	82	14	52	52	2	0	45	1.13
10282697--10282738	15	2.9	15	82	10	52	52	0	0	47	1.00
10282826--10282862	16	2.2	17	86	13	51	54	0	2	43	1.14
10282904--10282964	28	2.2	28	85	5	81	50	3	0	45	1.17
10282879--10283177	91	3.3	91	93	0	499	46	4	3	46	1.39
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10282845--10283177	47	7.3	44	67	16	137	46	4	3	45	1.38
10286706--10286747	15	2.7	16	82	14	52	52	2	0	45	1.13
10286715--10286756	15	2.9	15	82	10	52	52	0	0	47	1.00
10286825--10286876	15	3.6	15	80	12	56	53	1	0	44	1.11
10287185--10287236	15	3.6	15	80	12	56	53	1	0	44	1.11
10286709--10287361	120	5.4	120	95	1	1157	49	5	2	42	1.38
10287402--10287462	28	2.2	28	85	5	81	50	3	0	45	1.17
10287377--10287584	91	2.3	90	88	4	299	46	4	3	46	1.39
10287421--10287559	47	3.0	47	67	17	128	46	5	2	45	1.39
10288942--10288991	7	7.0	7	77	4	55	60	4	0	36	1.16
10289044--10289070	11	2.5	11	100	0	54	51	18	7	22	1.70
10291271--10291303	10	3.5	10	92	8	52	24	6	6	63	1.40
10291814--10291888	23	3.3	23	82	14	93	57	21	6	14	1.60
10291814--10291888	11	6.6	11	70	20	57	57	21	6	14	1.60
10295510--10295543	16	2.1	16	88	0	50	29	11	17	41	1.85
10298498--10298528	16	1.9	16	93	0	53	35	0	64	0	0.94
10301503--10301563	2	30.5	2	100	0	122	50	0	0	49	1.00
10308014--10308054	14	2.7	15	85	7	57	73	2	2	21	1.07
10308931--10308957	6	4.5	6	100	0	54	0	51	0	48	1.00
10315675--10315786	44	2.5	44	79	1	116	25	25	19	28	1.99
10315745--10316761	88	11.6	88	84	2	1028	24	25	23	26	2.00
10322897--10322940	14	3.0	14	83	6	52	65	0	2	31	1.05
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
10323003--10323030	2	14.0	2	100	0	56	50	0	0	50	1.00
10323082--10323147	35	1.9	34	87	3	96	57	3	3	36	1.29
10323069--10323174	29	3.4	31	75	16	94	57	5	2	33	1.37
10323410--10323450	3	13.3	3	85	14	57	63	0	0	36	0.95
10323414--10323456	18	2.4	18	88	7	61	62	2	0	34	1.08
10323407--10323456	21	2.4	21	81	18	68	62	4	0	34	1.14
10328161--10328251	3	30.3	3	93	0	128	62	2	4	30	1.27
10328624--10328667	23	1.9	23	85	0	61	29	4	4	61	1.36
10331795--10331827	17	1.9	17	100	0	66	54	6	0	39	1.25
10332051--10332104	3	17.7	3	92	3	90	64	0	1	33	1.04

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