genome.fa.s6.2.7.7.80.10.50.1000.102.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: Chr06 ID=Chr06-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  51074515

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   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   

This is table  102  of  168  ( 20060 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)
30028639--30028827	44	4.3	44	67	11	120	27	25	17	29	1.98
30028596--30028783	44	4.3	44	66	8	103	28	25	15	29	1.96
30030214--30030255	7	6.0	7	79	20	52	14	16	0	69	1.20
30031196--30031236	20	2.0	20	86	9	57	63	4	17	14	1.47
30034056--30034201	41	3.6	40	75	12	129	28	27	19	23	1.99
30034056--30034211	82	1.9	82	80	10	185	29	26	19	24	1.99
30038166--30038249	34	2.5	34	71	11	82	54	4	7	33	1.49
30038467--30038492	2	13.0	2	100	0	52	50	0	0	50	1.00
30048586--30048632	6	7.8	6	92	0	76	61	2	17	19	1.44
30054963--30055005	12	3.5	12	87	3	59	13	23	0	62	1.31
30054962--30055004	18	2.3	19	88	4	61	13	23	0	62	1.31
30065486--30065583	31	3.2	31	75	8	101	14	31	29	24	1.94
30070455--30070668	116	1.8	116	88	2	331	40	17	14	27	1.89
30077944--30078008	18	3.7	18	71	19	57	41	0	1	56	1.08
30077926--30077990	26	2.5	27	77	5	71	46	0	0	53	1.00
30077950--30078056	33	3.1	34	72	18	98	43	0	0	54	1.13
30077944--30078046	22	4.9	22	66	21	60	44	0	0	53	1.13
30078028--30078059	17	2.0	17	88	11	50	46	0	0	53	1.00
30078033--30078084	25	2.0	25	85	7	68	50	0	0	50	1.00
30077963--30078079	35	3.3	33	75	16	103	47	0	0	50	1.12
30079234--30079304	37	1.9	37	91	0	115	33	25	18	22	1.96
30079667--30079718	20	2.6	20	93	0	86	51	3	26	17	1.62
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30082588--30082705	36	3.3	36	82	4	132	42	27	11	17	1.85
30088310--30088494	13	14.2	13	68	12	65	36	17	4	42	1.69
30090819--30090843	13	1.9	13	100	0	50	16	0	8	76	1.02
30094748--30094772	1	25.0	1	100	0	50	100	0	0	0	0.00
30099526--30099566	2	20.5	2	100	0	82	51	0	0	48	1.00
30099674--30099714	2	20.5	2	100	0	82	51	0	0	48	1.00
30107775--30107833	31	1.9	31	92	0	100	33	15	11	38	1.84
30110007--30110036	6	5.0	6	95	0	51	53	0	13	33	1.40
30113046--30113082	15	2.5	15	86	0	56	56	0	0	43	0.99
30113150--30113194	19	2.2	20	84	7	56	28	6	4	60	1.42
30122091--30122130	21	1.9	21	90	10	64	50	0	0	50	1.00
30131289--30131355	32	2.2	30	89	5	98	58	2	1	37	1.23
30136040--30136108	26	2.7	25	82	4	93	17	28	21	31	1.96
30136076--30136215	73	1.9	73	85	2	192	20	25	20	33	1.97
30136219--30136285	25	2.7	25	90	0	98	28	26	13	31	1.94
30136174--30136293	25	4.9	25	76	3	82	23	26	18	31	1.97
30141299--30141485	85	2.2	84	89	2	277	46	10	11	31	1.74
30141320--30141649	182	1.8	179	82	9	427	45	10	11	32	1.74
30141525--30141914	88	4.4	87	83	7	382	41	10	14	34	1.80
30141525--30141914	175	2.2	175	80	8	418	41	10	14	34	1.80
30147145--30147184	21	1.9	21	89	0	62	27	2	25	45	1.66
30153339--30153440	31	3.3	31	84	0	114	29	9	26	34	1.88
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30153392--30153688	94	3.2	94	85	2	384	35	11	20	33	1.88
30153350--30153535	31	6.0	31	71	14	114	32	11	22	33	1.90
30153683--30153894	103	2.1	103	85	0	280	38	13	16	31	1.88
30158884--30158918	18	1.9	18	100	0	70	54	0	5	40	1.24
30159453--30159493	8	5.0	8	88	5	64	41	0	0	58	0.98
30159552--30159585	13	2.6	13	95	0	59	73	0	26	0	0.83
30160292--30160324	13	2.4	14	90	5	50	48	0	9	42	1.35
30160452--30160535	25	3.4	25	91	0	132	19	21	20	39	1.93
30160472--30160575	22	4.4	23	85	6	104	17	25	20	37	1.93
30160452--30160583	50	2.8	48	80	12	130	18	23	19	38	1.93
30163927--30163971	24	1.9	24	86	4	65	42	2	2	53	1.25
30165941--30165970	7	4.4	7	91	8	53	46	0	0	53	1.00
30179841--30179934	49	1.9	49	93	0	161	45	2	14	37	1.57
30181310--30181348	14	2.6	16	84	12	55	41	0	2	56	1.13
30181486--30181523	2	19.0	2	100	0	76	50	0	0	50	1.00
30186143--30186180	20	1.9	20	94	0	67	47	2	21	28	1.64
30186138--30186187	20	2.5	19	81	9	64	46	2	20	32	1.62
30186278--30186337	27	2.2	27	96	3	111	45	5	20	30	1.72
30198492--30198535	19	2.4	19	85	11	56	68	0	2	29	1.02
30204069--30204094	3	8.7	3	100	0	52	34	0	34	30	1.58
30204315--30204524	105	2.0	105	97	1	395	25	11	22	39	1.89
30212713--30212770	29	2.0	29	86	3	80	41	6	12	39	1.69
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30218220--30218275	28	2.0	28	92	0	94	28	10	10	50	1.71
30219490--30219524	14	2.5	14	95	0	61	34	20	5	40	1.76
30220748--30220915	62	2.7	61	92	1	264	49	8	5	36	1.57
30224139--30224217	27	2.9	27	80	0	104	22	32	25	18	1.97
30224297--30224327	3	10.3	3	92	0	53	29	0	3	67	1.06
30229877--30229919	21	2.0	21	86	0	59	16	25	18	39	1.91
30242671--30242767	28	3.5	28	91	0	149	31	26	10	30	1.90
30246289--30246321	5	6.8	5	86	6	50	21	0	0	78	0.75
30247937--30247966	14	2.1	15	93	6	53	26	0	0	73	0.84
30248093--30248173	21	3.8	21	75	14	76	64	0	1	34	1.02
30248568--30248635	35	1.9	35	84	0	91	35	8	13	42	1.75
30257124--30257205	37	2.2	37	88	0	119	59	1	3	35	1.23
30257124--30257205	18	4.4	19	70	4	60	59	1	3	35	1.23
30257416--30257479	21	3.0	21	68	17	51	32	4	0	62	1.16
30260479--30260540	31	2.0	31	100	0	124	32	9	16	41	1.80
30262547--30263430	437	2.0	437	95	0	1581	31	24	16	27	1.97
30272063--30272109	22	2.1	22	92	0	76	42	10	6	40	1.65
30275919--30275947	3	9.7	3	100	0	58	68	0	0	31	0.89
30276220--30276250	9	3.4	9	90	0	53	25	12	22	38	1.90
30276385--30276446	32	1.9	32	96	0	115	19	56	0	24	1.42
30278535--30278573	20	2.0	20	84	0	51	2	20	7	69	1.26
30290584--30290645	21	3.0	21	85	0	79	38	16	25	19	1.92
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30297209--30297253	21	2.1	22	84	12	58	66	8	11	13	1.44
30300045--30300222	34	5.2	34	84	2	221	40	17	23	19	1.91
30300058--30300223	35	4.8	34	85	2	215	39	18	23	19	1.92
30300058--30300222	69	2.4	69	93	0	285	38	18	23	19	1.93
30300419--30300474	18	3.3	18	76	19	75	35	12	7	44	1.70
30300420--30300484	32	2.0	32	100	0	130	38	12	6	43	1.67
30300427--30300480	17	3.3	17	75	19	69	42	12	5	38	1.67
30300502--30300536	14	2.6	14	95	4	63	37	14	5	42	1.69
30302831--30302858	6	4.7	6	100	0	56	53	0	0	46	1.00
30302973--30303023	3	17.0	3	79	0	57	58	5	3	31	1.40
30305228--30305257	13	2.3	13	94	0	51	33	13	3	50	1.58
30307747--30307835	31	3.0	30	78	4	90	32	13	14	39	1.85
30309277--30309571	43	6.9	43	85	2	351	29	31	15	23	1.95
30309277--30309572	86	3.4	86	87	0	412	29	31	15	23	1.95
30309944--30309988	21	2.1	21	91	0	72	2	44	15	37	1.59
30317292--30317339	2	24.0	2	86	0	69	43	0	6	50	1.27
30317293--30317345	8	6.6	8	91	0	61	43	0	7	49	1.31
30321218--30321265	9	4.9	9	76	18	51	35	0	16	47	1.47
30321911--30321982	29	2.5	30	76	19	80	50	1	2	45	1.25
30322417--30322450	2	17.0	2	100	0	68	50	0	0	50	1.00
30327644--30327871	110	2.0	111	85	5	300	45	14	13	26	1.82
30344833--30344861	15	1.9	15	100	0	58	20	0	24	55	1.44
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
30345013--30345046	17	1.9	18	88	5	52	38	5	0	55	1.24
30356103--30356145	21	2.2	18	84	12	50	32	2	0	65	1.06
30359636--30359663	13	2.2	13	100	0	56	78	0	7	14	0.95
30359646--30359687	17	2.5	17	88	11	61	78	4	2	14	1.01
30365809--30365907	28	3.5	28	84	4	110	31	11	28	29	1.91
30367927--30368002	36	2.0	39	87	7	113	60	0	1	38	1.05
30381377--30381461	44	1.9	45	85	7	120	30	36	11	21	1.89
30381477--30381542	13	5.1	13	77	0	78	31	7	25	34	1.84
30381712--30381773	30	2.1	29	82	11	72	46	0	3	50	1.17
30381724--30381828	33	3.1	33	75	19	92	51	0	0	46	1.13

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   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168