genome.fa.s3.2.7.7.80.10.50.1000.143.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  143  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)
43256354--43256394	17	2.3	18	80	12	50	31	2	2	63	1.20
43266678--43266720	18	2.4	18	88	7	61	53	0	0	46	1.00
43267788--43267853	28	2.3	29	82	10	73	59	6	0	34	1.22
43268155--43268208	9	6.2	9	81	12	60	35	1	0	62	1.06
43268157--43268207	24	2.1	25	88	3	77	31	1	0	66	1.03
43269599--43269633	17	1.9	19	88	11	56	34	0	25	40	1.56
43276608--43276648	2	20.5	2	94	0	73	48	0	2	48	1.14
43278970--43278998	2	14.5	2	100	0	58	51	0	0	48	1.00
43279275--43279321	15	3.1	15	90	0	58	55	0	10	34	1.35
43279289--43279321	12	2.8	12	95	0	57	57	0	9	33	1.30
43281071--43281682	87	7.1	87	72	12	433	28	22	19	29	1.98
43280999--43281770	43	18.0	44	70	13	400	27	22	20	30	1.98
43281009--43281778	173	4.5	174	88	4	1118	27	22	20	30	1.98
43283878--43283917	21	2.0	20	90	5	62	5	15	0	80	0.88
43288305--43288333	2	14.5	2	100	0	58	51	0	0	48	1.00
43288610--43288656	15	3.1	15	90	0	58	55	0	10	34	1.35
43288624--43288656	12	2.8	12	95	0	57	57	0	9	33	1.30
43293778--43293879	38	2.7	38	76	0	105	35	19	12	32	1.90
43296205--43296239	5	7.0	5	90	0	52	22	0	2	74	0.95
43297868--43297899	14	2.3	14	94	0	55	15	15	15	53	1.74
43312712--43312741	15	1.9	16	93	6	53	43	0	6	50	1.28
43312733--43312767	18	2.0	17	88	5	52	45	0	0	54	0.99
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43312914--43313019	39	2.5	44	82	10	123	33	29	4	32	1.78
43312927--43313019	44	2.1	46	87	4	136	35	27	5	31	1.80
43313001--43313038	16	2.4	16	90	0	58	26	31	2	39	1.70
43316919--43317026	5	22.4	5	68	20	52	58	1	2	37	1.23
43316942--43317012	30	2.3	30	78	21	76	54	1	2	40	1.23
43319937--43320091	72	2.2	72	88	2	222	29	28	16	25	1.97
43319937--43320115	72	2.5	72	82	7	204	31	26	16	25	1.97
43334826--43334869	16	2.8	15	80	10	52	34	6	0	59	1.24
43336251--43336284	2	17.5	2	93	6	61	50	0	0	50	1.00
43347664--43347707	2	22.5	2	95	4	81	50	0	0	50	1.00
43347924--43347988	21	3.1	21	90	0	103	40	7	10	41	1.69
43348226--43348270	23	2.0	23	81	0	54	22	0	15	62	1.33
43360287--43360341	21	2.8	19	81	13	58	29	1	3	65	1.20
43368368--43368407	20	2.0	20	90	0	62	50	12	10	27	1.72
43368356--43368422	34	1.9	35	87	3	100	47	10	8	32	1.69
43370123--43370150	13	2.2	13	100	0	56	35	14	0	50	1.43
43378520--43378565	2	23.0	2	90	0	74	50	4	0	45	1.21
43380442--43380500	28	2.1	29	81	9	68	57	1	3	37	1.25
43381104--43381147	19	2.3	19	80	7	54	36	0	2	61	1.09
43392705--43392794	31	3.0	31	84	9	114	40	7	12	40	1.71
43396440--43396501	11	5.5	11	83	9	72	29	1	0	69	0.98
43398804--43398843	21	1.9	21	94	0	71	45	10	0	45	1.37
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43398833--43398884	17	3.1	17	83	5	61	82	7	0	9	0.84
43398841--43398882	16	2.7	16	88	3	59	88	4	0	7	0.64
43398913--43398989	27	2.9	27	94	0	127	25	28	31	14	1.95
43399034--43399084	18	2.8	18	87	3	66	25	0	7	66	1.18
43399082--43399115	17	2.0	17	100	0	68	41	0	17	41	1.50
43399125--43399193	28	2.5	28	88	2	104	42	8	0	49	1.34
43399195--43399239	18	2.3	20	88	7	67	84	4	4	6	0.87
43399908--43399976	28	2.5	29	88	6	108	47	0	10	42	1.37
43400000--43400039	19	2.2	18	90	4	62	70	5	0	25	1.08
43400000--43400050	18	2.7	19	87	3	68	66	7	0	25	1.18
43400095--43400171	27	2.9	27	94	0	127	14	31	28	25	1.95
43400200--43400242	1	43.0	1	80	0	50	2	0	6	90	0.52
43400203--43400241	8	4.9	8	87	12	62	2	0	7	89	0.56
43400202--43400243	17	2.5	17	92	3	68	2	0	9	88	0.61
43400200--43400243	16	2.7	16	89	3	70	2	0	9	88	0.59
43400199--43400253	27	2.0	27	82	6	67	7	0	10	81	0.86
43400244--43400312	28	2.4	29	85	4	97	49	1	8	40	1.43
43403657--43403722	33	2.0	33	85	5	89	40	24	12	22	1.88
43404952--43405016	29	2.2	29	83	2	76	43	4	6	46	1.49
43405848--43405916	27	2.5	28	90	6	106	39	10	1	49	1.46
43405986--43406059	27	2.7	27	85	0	85	31	24	35	9	1.87
43406021--43406084	27	2.4	27	83	0	74	20	29	34	15	1.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43406368--43406423	3	18.7	3	100	0	112	33	0	0	66	0.92
43407229--43407277	21	2.3	21	100	0	98	28	18	26	26	1.98
43411633--43411674	17	2.4	18	88	11	61	4	4	4	85	0.82
43411676--43411745	28	2.5	29	90	4	117	48	0	11	40	1.39
43411750--43411774	13	1.9	13	100	0	50	16	0	4	80	0.87
43412607--43412654	24	2.0	24	87	4	69	2	25	0	72	0.95
43412645--43412745	10	10.5	10	68	16	70	1	33	0	64	1.05
43412652--43412747	18	5.3	18	72	14	72	2	32	0	65	1.04
43412588--43412766	76	2.4	73	76	12	170	1	30	0	67	1.04
43412644--43412731	38	2.3	38	94	0	149	2	35	0	62	1.08
43412689--43412762	14	5.1	14	72	22	55	0	31	0	68	0.89
43412683--43412762	34	2.8	28	75	24	85	0	32	0	67	0.91
43412588--43412765	10	16.7	10	66	19	58	1	29	0	67	1.04
43412641--43412753	38	3.0	38	88	2	147	1	34	0	63	1.05
43412723--43412765	22	1.9	23	85	4	61	0	30	0	69	0.88
43412685--43412766	28	2.7	30	75	19	89	0	32	0	67	0.91
43412664--43412779	42	2.9	40	80	10	105	0	36	0	63	0.94
43412921--43412958	8	4.8	8	84	12	51	7	2	2	86	0.74
43412960--43413028	28	2.5	29	90	6	108	49	1	10	39	1.46
43414979--43415047	23	3.0	23	75	12	68	1	24	0	73	0.91
43414960--43415118	38	4.3	38	82	11	172	0	30	0	69	0.94
43414960--43415116	10	15.9	10	68	17	80	0	30	0	68	0.94
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43414960--43415133	18	9.4	18	69	19	101	0	30	0	68	0.93
43415060--43415133	14	5.1	14	72	22	55	0	31	0	68	0.89
43415054--43415133	34	2.8	28	75	24	85	0	32	0	67	0.91
43414960--43415136	10	16.7	10	67	18	65	0	30	0	68	0.93
43415094--43415136	22	1.9	23	85	4	61	0	30	0	69	0.88
43415056--43415137	28	2.7	30	75	19	89	0	32	0	67	0.91
43415035--43415150	42	2.9	40	80	10	105	0	36	0	63	0.94
43418467--43418509	22	1.9	22	90	4	68	37	0	2	60	1.10
43419209--43419274	33	2.0	33	88	5	98	42	24	10	22	1.85
43420776--43420840	29	2.2	29	83	2	76	44	4	3	47	1.39
43423703--43423728	2	13.0	2	100	0	52	50	0	0	50	1.00
43423831--43423855	13	1.9	13	100	0	50	64	4	0	32	1.12
43423883--43423950	13	5.8	12	74	19	54	66	7	0	26	1.18
43423883--43423924	17	2.6	17	85	14	54	69	7	0	23	1.13
43424510--43424570	30	2.0	30	81	12	72	80	4	1	13	0.95
43424518--43424570	10	5.3	9	78	17	52	81	3	1	13	0.92
43427432--43427494	33	1.9	33	83	6	83	39	23	12	23	1.89
43429983--43430022	21	2.0	20	90	5	62	57	5	0	37	1.21
43430183--43430257	13	5.8	13	80	0	87	37	22	6	33	1.80
43430186--43430259	26	2.8	26	85	0	103	39	24	6	29	1.81
43436427--43436477	6	8.2	6	77	16	50	21	3	0	74	0.98
43440578--43440637	18	3.6	17	80	8	61	58	3	5	33	1.36
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
43440578--43440637	15	3.6	16	80	10	59	58	3	5	33	1.36
43444267--43444304	2	19.0	2	94	0	67	50	2	47	0	1.15
43445745--43445773	6	4.8	6	100	0	58	0	0	17	82	0.66
43446724--43446763	16	2.3	18	91	8	66	42	5	0	52	1.23
43447054--43447098	22	2.0	22	83	8	56	64	2	2	31	1.18
43448224--43448277	19	2.8	20	76	21	60	35	0	1	62	1.06
43448186--43448297	48	2.4	47	78	11	113	37	1	1	58	1.19
43448165--43448277	10	11.6	10	71	17	62	36	0	3	59	1.21
43448224--43448311	10	9.2	9	75	21	65	34	2	2	61	1.21
43448412--43448437	9	2.9	9	100	0	52	23	11	34	30	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